Changes between Initial Version and Version 1 of Ticket #4877


Ignore:
Timestamp:
Jul 9, 2021, 11:13:02 AM (4 years ago)
Author:
Tom Goddard
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #4877

    • Property Component Unassigned → Structure Analysis
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → addh failed: TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'

  • Ticket #4877 – Description

    initial v1  
    101101> wait 5
    102102
    103 > contacts :UNL radius 0.05 log true saveFile
    104 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
    105 > WRM-16.contacts.txt
    106    
    107    
    108     Allowed overlap: -0.4
    109     H-bond overlap reduction: 0.4
    110     Ignore contacts between atoms separated by 4 bonds or less
    111     Detect intra-residue contacts: False
    112     Detect intra-molecule contacts: True
    113    
    114     40 contacts
    115                       atom1                               atom2              overlap  distance
    116     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C ARG 639 HE     0.326    2.554
    117     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 458 O      0.049    3.311
    118     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C ARG 639 NE     -0.005    3.510
    119     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C LEU 410 HN     -0.006    2.886
    120     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 HB2    -0.009    2.889
    121     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 638 O      -0.028    3.388
    122     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C ILE 591 HN     -0.045    2.065
    123     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ALA 501 O      -0.050    3.410
    124     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C LEU 410 O      -0.056    3.416
    125     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ARG 639 HG2    -0.071    2.831
    126     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C VAL 637 CG1    -0.071    3.531
    127     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C VAL 637 2HG1   -0.089    2.509
    128     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ALA 501 C      -0.092    3.672
    129     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 592 HB2    -0.115    2.995
    130     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 592 CB     -0.121    3.701
    131     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 HD2    -0.131    2.891
    132     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C SER 590 HA     -0.193    2.613
    133     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ALA 501 HB2    -0.227    3.107
    134     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C TYR 678 HD2    -0.237    2.997
    135     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ARG 639 CG     -0.240    3.700
    136     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C TYR 678 CD2    -0.246    3.706
    137     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ILE 591 O      -0.258    3.618
    138     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ARG 639 HE     -0.271    3.031
    139     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C ILE 591 O      -0.284    3.184
    140     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C ILE 591 O      -0.286    3.226
    141     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 CD2    -0.291    3.751
    142     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 CD2    -0.291    3.751
    143     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 638 HB2    -0.296    3.176
    144     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 HD2    -0.312    3.072
    145     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C MET 679 O      -0.331    3.691
    146     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C ARG 639 2HH2   -0.331    3.211
    147     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C SER 590 CA     -0.344    3.464
    148     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C VAL 637 2HG1   -0.350    3.110
    149     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 638 C      -0.357    3.937
    150     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C ALA 501 CB     -0.367    3.947
    151     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O   3EI4.pdbqt #1/C ILE 591 N      -0.374    3.019
    152     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C VAL 637 CG1    -0.386    3.696
    153     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3EI4.pdbqt #1/C LEU 410 N      -0.387    3.892
    154     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C PHE 459 CB     -0.394    3.974
    155     3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C   3EI4.pdbqt #1/C LEU 592 HB1    -0.394    3.274
    156    
    157 
    158  
    159 40 contacts 
    160 
    161 > hbonds :UNL showDist true radius 0.05 log true saveFile
    162 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
    163 > WRM-16.hbonds.txt
    164    
    165    
    166     Finding intermodel H-bonds
    167     Finding intramodel H-bonds
    168     Constraints relaxed by 0.4 angstroms and 20 degrees
    169     Models used:
    170         1 3EI4.pdbqt
    171         2.1 3EI4--WRM-16.result.pdbqt
    172    
    173     1 H-bonds
    174     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    175     3EI4.pdbqt #1/C ILE 591 N  3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O  3EI4.pdbqt #1/C ILE 591 HN  3.019  2.065
    176    
    177 
    178  
    179 1 hydrogen bonds found 
    180 
    181 > select :UNL
    182 
    183 28 atoms, 31 bonds, 1 residue, 1 model selected 
    184 
    185 > label sel text "Ligand "
    186 
    187 > label height 1
    188 
    189 > ~select
    190 
    191 Nothing selected 
    192 
    193 > 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
    194 > ypos .95
    195 
    196 > 2dlabels text "3EI4 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    197 
    198 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
    199 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    200 > true
    201 
    202 > select :UNL
    203 
    204 28 atoms, 31 bonds, 1 residue, 1 model selected 
    205 
    206 > view sel
    207 
    208 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
    209 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    210 > true
    211 
    212 > close
    213 
    214 > wait 5
    215 
    216 > set bgColor white
    217 
    218 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2PA2.pdbqt
    219 
    220 Chain information for 2PA2.pdbqt #1 
    221 --- 
    222 Chain | Description 
    223 A B | No description available 
    224  
    225 Opened 2PA2.pdbqt containing 1 structures (3578 atoms, 3614 bonds) 
    226 
    227 > wait 5
    228 
    229 > hide surfaces
    230 
    231 > hide atoms
    232 
    233 > show cartoons
    234 
    235 > wait 5
    236 
    237 > addh
    238 
    239 Summary of feedback from adding hydrogens to 2PA2.pdbqt #1 
    240 --- 
    241 notes | No usable SEQRES records for 2PA2.pdbqt (#1) chain A; guessing termini
    242 instead 
    243 No usable SEQRES records for 2PA2.pdbqt (#1) chain B; guessing termini instead 
    244 Chain-initial residues that are actual N termini: /A LYS 40, /B LYS 40 
    245 Chain-initial residues that are not actual N termini: /A GLY 124, /B GLY 124 
    246 Chain-final residues that are actual C termini: /A PHE 176, /B PHE 176 
    247 Chain-final residues that are not actual C termini: /A PHE 94, /B PHE 94 
    248 173 hydrogen bonds 
    249 Adding 'H' to /A GLY 124 
    250 Adding 'H' to /B GLY 124 
    251 /A PHE 94 is not terminus, removing H atom from 'C' 
    252 /B PHE 94 is not terminus, removing H atom from 'C' 
    253 0 hydrogens added 
    254  
    255 
    256 > wait 5
    257 
    258 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--
    259 > WRM-16.result.pdbqt
    260 
    261 Summary of feedback from opening
    262 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--WRM-16.result.pdbqt 
    263 --- 
    264 warnings | Ignored bad PDB record found on line 2 
    265 REMARK VINA RESULT: -8.4 0.000 0.000 
    266  
    267 Ignored bad PDB record found on line 3 
    268 REMARK 5 active torsions: 
    269  
    270 Ignored bad PDB record found on line 4 
    271 REMARK status: ('A' for Active; 'I' for Inactive) 
    272  
    273 Ignored bad PDB record found on line 5 
    274 REMARK 1 A between atoms: C_9 and O_15 
    275  
    276 Ignored bad PDB record found on line 6 
    277 REMARK 2 A between atoms: C_10 and O_17 
    278  
    279 184 messages similar to the above omitted 
    280  
    281 Opened 2PA2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    282 bonds) 
    283 
    284 > wait 5
    285 
    286 > close #2.2-9
    287 
    288 > wait 5
    289 
    290 > contacts :UNL radius 0.05 log true saveFile
    291 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
    292 > WRM-16.contacts.txt
    293    
    294    
    295     Allowed overlap: -0.4
    296     H-bond overlap reduction: 0.4
    297     Ignore contacts between atoms separated by 4 bonds or less
    298     Detect intra-residue contacts: False
    299     Detect intra-molecule contacts: True
    300    
    301     42 contacts
    302                       atom1                               atom2              overlap  distance
    303     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A ARG 139 1HH1   0.226    2.384
    304     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A ARG 139 1HH1   0.203    1.817
    305     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 HE2    0.129    2.481
    306     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B ARG 128 HB2    0.110    2.650
    307     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 HE1    0.107    2.773
    308     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HB2    0.007    2.753
    309     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 HE2    0.001    2.759
    310     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HB2    -0.038    2.648
    311     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 HE2    -0.039    2.649
    312     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A ARG 139 1HH2   -0.042    2.922
    313     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A ARG 139 1HH2   -0.049    2.109
    314     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2PA2.pdbqt #1/B HIS 92 O       -0.078    3.438
    315     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 CE1    -0.094    3.674
    316     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A ARG 139 1HH2   -0.105    2.985
    317     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A VAL 43 CG1     -0.107    3.687
    318     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A PRO 47 HA      -0.111    2.531
    319     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HD1    -0.114    2.874
    320     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HD1    -0.119    2.879
    321     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2PA2.pdbqt #1/B ARG 128 O      -0.121    3.481
    322     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/B HIS 130 HE1    -0.121    2.581
    323     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A ARG 139 NH1    -0.139    2.784
    324     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A ARG 139 NH1    -0.150    3.385
    325     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 NE2    -0.172    3.557
    326     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HB2    -0.175    2.785
    327     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 CD1    -0.211    3.671
    328     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A LYS 169 O      -0.229    3.319
    329     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A ARG 139 NH2    -0.235    3.740
    330     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A VAL 43 O       -0.237    3.137
    331     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 NE2    -0.243    3.478
    332     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B ARG 128 HD2    -0.251    3.011
    333     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 CB     -0.266    3.576
    334     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2PA2.pdbqt #1/A TRP 171 HB2    -0.278    2.698
    335     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A PRO 47 CB      -0.283    3.863
    336     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B ARG 128 CB     -0.291    3.751
    337     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A VAL 43 1HG1    -0.297    3.177
    338     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2PA2.pdbqt #1/B HIS 92 HN      -0.300    3.180
    339     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 CD1    -0.306    3.766
    340     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 CB     -0.325    3.785
    341     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 NE2    -0.331    3.566
    342     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A TRP 171 HN     -0.354    3.234
    343     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/A VAL 43 HB      -0.364    2.974
    344     2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2PA2.pdbqt #1/B HIS 130 HE2    -0.383    3.143
    345    
    346 
    347  
    348 42 contacts 
    349 
    350 > hbonds :UNL showDist true radius 0.05 log true saveFile
    351 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
    352 > WRM-16.hbonds.txt
    353    
    354    
    355     Finding intermodel H-bonds
    356     Finding intramodel H-bonds
    357     Constraints relaxed by 0.4 angstroms and 20 degrees
    358     Models used:
    359         1 2PA2.pdbqt
    360         2.1 2PA2--WRM-16.result.pdbqt
    361    
    362     4 H-bonds
    363     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    364     2PA2.pdbqt #1/A ARG 139 NH1  2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O  2PA2.pdbqt #1/A ARG 139 1HH1  3.380  2.525
    365     2PA2.pdbqt #1/A ARG 139 NH1  2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O  2PA2.pdbqt #1/A ARG 139 1HH1  2.784  1.817
    366     2PA2.pdbqt #1/A ARG 139 NH2  2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O  2PA2.pdbqt #1/A ARG 139 1HH2  3.087  2.109
    367     2PA2.pdbqt #1/A TRP 171 N    2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O  2PA2.pdbqt #1/A TRP 171 HN    3.576  2.621
    368    
    369 
    370  
    371 4 hydrogen bonds found 
    372 
    373 > select :UNL
    374 
    375 28 atoms, 31 bonds, 1 residue, 1 model selected 
    376 
    377 > label sel text "Ligand "
    378 
    379 > label height 1
    380 
    381 > ~select
    382 
    383 Nothing selected 
    384 
    385 > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
    386 > ypos .95
    387 
    388 > 2dlabels text "2PA2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    389 
    390 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
    391 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    392 > true
    393 
    394 > select :UNL
    395 
    396 28 atoms, 31 bonds, 1 residue, 1 model selected 
    397 
    398 > view sel
    399 
    400 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
    401 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    402 > true
    403 
    404 > close
    405 
    406 > wait 5
    407 
    408 > set bgColor white
    409 
    410 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KV2.pdbqt
    411 
    412 Chain information for 2KV2.pdbqt #1 
    413 --- 
    414 Chain | Description 
    415 A | No description available 
    416  
    417 Opened 2KV2.pdbqt containing 1 structures (1351 atoms, 1361 bonds) 
    418 
    419 > wait 5
    420 
    421 > hide surfaces
    422 
    423 > hide atoms
    424 
    425 > show cartoons
    426 
    427 > wait 5
    428 
    429 > addh
    430 
    431 Summary of feedback from adding hydrogens to 2KV2.pdbqt #1 
    432 --- 
    433 notes | No usable SEQRES records for 2KV2.pdbqt (#1) chain A; guessing termini
    434 instead 
    435 Chain-initial residues that are actual N termini: /A GLN 1 
    436 Chain-initial residues that are not actual N termini: 
    437 Chain-final residues that are actual C termini: /A ASP 85 
    438 Chain-final residues that are not actual C termini: 
    439 61 hydrogen bonds 
    440 1 hydrogens added 
    441  
    442 
    443 > wait 5
    444 
    445 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--
    446 > WRM-16.result.pdbqt
    447 
    448 Summary of feedback from opening
    449 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--WRM-16.result.pdbqt 
    450 --- 
    451 warnings | Ignored bad PDB record found on line 2 
    452 REMARK VINA RESULT: -6.4 0.000 0.000 
    453  
    454 Ignored bad PDB record found on line 3 
    455 REMARK 5 active torsions: 
    456  
    457 Ignored bad PDB record found on line 4 
    458 REMARK status: ('A' for Active; 'I' for Inactive) 
    459  
    460 Ignored bad PDB record found on line 5 
    461 REMARK 1 A between atoms: C_9 and O_15 
    462  
    463 Ignored bad PDB record found on line 6 
    464 REMARK 2 A between atoms: C_10 and O_17 
    465  
    466 184 messages similar to the above omitted 
    467  
    468 Opened 2KV2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    469 bonds) 
    470 
    471 > wait 5
    472 
    473 > close #2.2-9
    474 
    475 > wait 5
    476 
    477 > contacts :UNL radius 0.05 log true saveFile
    478 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
    479 > WRM-16.contacts.txt
    480    
    481    
    482     Allowed overlap: -0.4
    483     H-bond overlap reduction: 0.4
    484     Ignore contacts between atoms separated by 4 bonds or less
    485     Detect intra-residue contacts: False
    486     Detect intra-molecule contacts: True
    487    
    488     52 contacts
    489                       atom1                               atom2             overlap  distance
    490     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HB2    0.640    2.240
    491     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 HB3    0.469    2.291
    492     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 CB     0.306    3.274
    493     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HD2    0.278    2.482
    494     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A THR 80 HB     0.207    2.673
    495     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 8 CE      0.105    3.055
    496     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 HD2    0.105    2.655
    497     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 CB     0.100    3.360
    498     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 HB2    0.075    2.685
    499     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A THR 80 CB     0.039    3.541
    500     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 CD2    -0.031    3.491
    501     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 HE3    -0.057    2.817
    502     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 HD1    -0.060    2.820
    503     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CE3    -0.080    3.540
    504     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CD1    -0.084    3.544
    505     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 HZ3    -0.099    2.979
    506     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CD1    -0.106    3.686
    507     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A THR 80 HB     -0.115    2.875
    508     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HB2    -0.131    3.011
    509     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 8 HE2     -0.136    2.596
    510     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HA     -0.165    2.775
    511     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HA     -0.207    2.817
    512     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 CD     -0.208    3.668
    513     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A THR 80 OG1    -0.214    3.594
    514     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CB     -0.214    3.674
    515     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 HB3    -0.227    2.837
    516     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CE3    -0.237    3.547
    517     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HD2    -0.262    3.142
    518     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 C      -0.263    3.723
    519     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A TRP 79 CE3    -0.272    3.852
    520     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A TRP 79 CZ3    -0.273    3.853
    521     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A TRP 79 HZ3    -0.277    3.157
    522     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KV2.pdbqt #1/A TRP 79 HE3    -0.280    3.160
    523     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 CB     -0.297    3.607
    524     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 CD2    -0.310    3.890
    525     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 CB     -0.317    3.897
    526     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 O      -0.323    3.563
    527     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 8 HE2     -0.324    2.744
    528     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 75 HB3    -0.325    2.785
    529     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 O      -0.329    3.569
    530     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 75 CB     -0.330    3.490
    531     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HB2    -0.331    2.941
    532     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 O      -0.336    3.576
    533     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A TRP 79 CG     -0.355    3.515
    534     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 HE3    -0.360    2.970
    535     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 NZ     -0.373    3.878
    536     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TRP 79 CG     -0.376    3.956
    537     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A VAL 72 3HG2   -0.383    2.803
    538     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KV2.pdbqt #1/A LYS 8 HE3     -0.388    2.848
    539     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A TYR 76 HD2    -0.388    3.148
    540     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 75 HB3    -0.391    3.151
    541     2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KV2.pdbqt #1/A LYS 8 HE2     -0.399    3.009
    542    
    543 
    544  
    545 52 contacts 
    546 
    547 > hbonds :UNL showDist true radius 0.05 log true saveFile
    548 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
    549 > WRM-16.hbonds.txt
    550    
    551    
    552     Finding intermodel H-bonds
    553     Finding intramodel H-bonds
    554     Constraints relaxed by 0.4 angstroms and 20 degrees
    555     Models used:
    556         1 2KV2.pdbqt
    557         2.1 2KV2--WRM-16.result.pdbqt
    558    
    559     0 H-bonds
    560     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    561    
    562 
    563  
    564 0 hydrogen bonds found 
    565 
    566 > select :UNL
    567 
    568 28 atoms, 31 bonds, 1 residue, 1 model selected 
    569 
    570 > label sel text "Ligand "
    571 
    572 > label height 1
    573 
    574 > ~select
    575 
    576 Nothing selected 
    577 
    578 > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
    579 > ypos .95
    580 
    581 > 2dlabels text "2KV2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    582 
    583 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
    584 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    585 > true
    586 
    587 > select :UNL
    588 
    589 28 atoms, 31 bonds, 1 residue, 1 model selected 
    590 
    591 > view sel
    592 
    593 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
    594 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    595 > true
    596 
    597 > close
    598 
    599 > wait 5
    600 
    601 > set bgColor white
    602 
    603 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3CO6.pdbqt
    604 
    605 Chain information for 3CO6.pdbqt #1 
    606 --- 
    607 Chain | Description 
    608 A | No description available 
    609 B | No description available 
    610 C | No description available 
    611  
    612 Opened 3CO6.pdbqt containing 1 structures (2476 atoms, 2572 bonds) 
    613 
    614 > wait 5
    615 
    616 > hide surfaces
    617 
    618 > hide atoms
    619 
    620 > show cartoons
    621 
    622 > wait 5
    623 
    624 > addh
    625 
    626 Summary of feedback from adding hydrogens to 3CO6.pdbqt #1 
    627 --- 
    628 warnings | Not adding hydrogens to /C LYS 192 CB because it is missing heavy-
    629 atom bond partners 
    630 Not adding hydrogens to /C LYS 198 CB because it is missing heavy-atom bond
    631 partners 
    632 Not adding hydrogens to /C ASN 204 CB because it is missing heavy-atom bond
    633 partners 
    634 Not adding hydrogens to /C GLU 242 CB because it is missing heavy-atom bond
    635 partners 
    636 notes | No usable SEQRES records for 3CO6.pdbqt (#1) chain A; guessing termini
    637 instead 
    638 No usable SEQRES records for 3CO6.pdbqt (#1) chain B; guessing termini instead 
    639 No usable SEQRES records for 3CO6.pdbqt (#1) chain C; guessing termini instead 
    640 Chain-initial residues that are actual N termini: /A DT -4, /B DC 13, /C SER
    641 154 
    642 Chain-initial residues that are not actual N termini: 
    643 Chain-final residues that are actual C termini: /A DG 12, /B DA 28, /C GLY 244 
    644 Chain-final residues that are not actual C termini: 
    645 127 hydrogen bonds 
    646 4 hydrogens added 
    647  
    648 
    649 > wait 5
    650 
    651 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--
    652 > WRM-16.result.pdbqt
    653 
    654 Summary of feedback from opening
    655 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--WRM-16.result.pdbqt 
    656 --- 
    657 warnings | Ignored bad PDB record found on line 2 
    658 REMARK VINA RESULT: -9.1 0.000 0.000 
    659  
    660 Ignored bad PDB record found on line 3 
    661 REMARK 5 active torsions: 
    662  
    663 Ignored bad PDB record found on line 4 
    664 REMARK status: ('A' for Active; 'I' for Inactive) 
    665  
    666 Ignored bad PDB record found on line 5 
    667 REMARK 1 A between atoms: C_9 and O_15 
    668  
    669 Ignored bad PDB record found on line 6 
    670 REMARK 2 A between atoms: C_10 and O_17 
    671  
    672 184 messages similar to the above omitted 
    673  
    674 Opened 3CO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    675 bonds) 
    676 
    677 > wait 5
    678 
    679 > close #2.2-9
    680 
    681 > wait 5
    682 
    683 > contacts :UNL radius 0.05 log true saveFile
    684 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
    685 > WRM-16.contacts.txt
    686    
    687    
    688     Allowed overlap: -0.4
    689     H-bond overlap reduction: 0.4
    690     Ignore contacts between atoms separated by 4 bonds or less
    691     Detect intra-residue contacts: False
    692     Detect intra-molecule contacts: True
    693    
    694     57 contacts
    695                       atom1                               atom2              overlap  distance
    696     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3CO6.pdbqt #1/A DT 4 H4'       0.285    2.595
    697     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 234 HA     0.279    2.481
    698     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C GLN 227 OE1    0.215    3.025
    699     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 O3'      0.090    3.290
    700     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C ARG 225 2HH1   0.039    2.721
    701     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C ARG 225 NH1    0.011    3.374
    702     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 C5'      0.002    3.578
    703     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 24 H3       0.000    2.880
    704     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 O4'       -0.016    3.396
    705     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DC 26 H4'      -0.026    2.906
    706     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 1H5'     -0.041    2.921
    707     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 C2       -0.066    3.226
    708     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 234 CA     -0.080    3.540
    709     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 H22       -0.090    2.850
    710     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 H3       -0.095    2.155
    711     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C LYS 233 O      -0.116    3.356
    712     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3CO6.pdbqt #1/A DT 4 C4'       -0.123    3.703
    713     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 H3        -0.125    2.885
    714     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 235 OG     -0.180    3.440
    715     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 H22       -0.187    2.947
    716     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DT 4 H4'       -0.190    2.800
    717     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 23 H2       -0.212    2.632
    718     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 2H5'     -0.212    3.092
    719     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 235 OG     -0.222    3.482
    720     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 N3       -0.223    2.908
    721     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 23 C2       -0.223    3.343
    722     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DC 26 C4'      -0.229    3.809
    723     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 C4'       -0.230    3.810
    724     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 H2       -0.237    2.697
    725     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DC 26 P        -0.239    3.990
    726     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/A DT 2 O4'       -0.260    3.180
    727     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/A DT 2 H4'       -0.264    2.724
    728     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 H4'      -0.269    2.879
    729     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C LYS 233 O      -0.273    3.513
    730     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 24 N3       -0.286    3.791
    731     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 O4'      -0.296    3.216
    732     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 H2       -0.297    2.717
    733     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DT 4 C4'       -0.299    3.759
    734     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C GLN 227 CD     -0.302    3.762
    735     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 H4'      -0.308    2.918
    736     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 N3        -0.316    3.701
    737     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 H4'       -0.322    3.202
    738     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DG 3 N2        -0.323    3.708
    739     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DT 4 H4'       -0.326    3.086
    740     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C ARG 225 NH1    -0.332    3.717
    741     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 C4       -0.337    3.457
    742     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/A DT 2 O2        -0.341    3.281
    743     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C ARG 225 2HH1   -0.352    3.112
    744     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DT 4 O4'       -0.360    3.620
    745     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 N3       -0.360    3.005
    746     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DC 26 C5'      -0.366    3.946
    747     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/A DT 4 C4'       -0.374    3.684
    748     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 235 N      -0.392    3.777
    749     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O   3CO6.pdbqt #1/B DA 24 C1'      -0.394    3.514
    750     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/C SER 235 N      -0.394    3.779
    751     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DC 26 OP1      -0.397    3.777
    752     3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C   3CO6.pdbqt #1/B DA 25 C4'      -0.400    3.980
    753    
    754 
    755  
    756 57 contacts 
    757 
    758 > hbonds :UNL showDist true radius 0.05 log true saveFile
    759 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
    760 > WRM-16.hbonds.txt
    761    
    762    
    763     Finding intermodel H-bonds
    764     Finding intramodel H-bonds
    765     Constraints relaxed by 0.4 angstroms and 20 degrees
    766     Models used:
    767         1 3CO6.pdbqt
    768         2.1 3CO6--WRM-16.result.pdbqt
    769    
    770     1 H-bonds
    771     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    772     3CO6.pdbqt #1/B DA 24 N3  3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O  3CO6.pdbqt #1/B DA 24 H3  2.908  2.155
    773    
    774 
    775  
    776 1 hydrogen bonds found 
    777 
    778 > select :UNL
    779 
    780 28 atoms, 31 bonds, 1 residue, 1 model selected 
    781 
    782 > label sel text "Ligand "
    783 
    784 > label height 1
    785 
    786 > ~select
    787 
    788 Nothing selected 
    789 
    790 > 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
    791 > ypos .95
    792 
    793 > 2dlabels text "3CO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    794 
    795 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
    796 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    797 > true
    798 
    799 > select :UNL
    800 
    801 28 atoms, 31 bonds, 1 residue, 1 model selected 
    802 
    803 > view sel
    804 
    805 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
    806 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    807 > true
    808 
    809 > close
    810 
    811 > wait 5
    812 
    813 > set bgColor white
    814 
    815 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1D7G.pdbqt
    816 
    817 Chain information for 1D7G.pdbqt #1 
    818 --- 
    819 Chain | Description 
    820 A | No description available 
    821 B | No description available 
    822 C | No description available 
    823 D | No description available 
    824  
    825 Opened 1D7G.pdbqt containing 1 structures (2929 atoms, 3008 bonds) 
    826 
    827 > wait 5
    828 
    829 > hide surfaces
    830 
    831 > hide atoms
    832 
    833 > show cartoons
    834 
    835 > wait 5
    836 
    837 > addh
    838 
    839 Summary of feedback from adding hydrogens to 1D7G.pdbqt #1 
    840 --- 
    841 warnings | Not adding hydrogens to /A G 5 C2' because it is missing heavy-atom
    842 bond partners 
    843 Not adding hydrogens to /A C 6 C2' because it is missing heavy-atom bond
    844 partners 
    845 Not adding hydrogens to /A C 7 C2' because it is missing heavy-atom bond
    846 partners 
    847 Not adding hydrogens to /A C 8 C2' because it is missing heavy-atom bond
    848 partners 
    849 Not adding hydrogens to /A A 10 C2' because it is missing heavy-atom bond
    850 partners 
    851 19 messages similar to the above omitted 
    852 notes | No usable SEQRES records for 1D7G.pdbqt (#1) chain A; guessing termini
    853 instead 
    854 No usable SEQRES records for 1D7G.pdbqt (#1) chain B; guessing termini instead 
    855 No usable SEQRES records for 1D7G.pdbqt (#1) chain C; guessing termini instead 
    856 No usable SEQRES records for 1D7G.pdbqt (#1) chain D; guessing termini instead 
    857 Chain-initial residues that are actual N termini: /A G 5, /B G 5, /C GLU 1, /D
    858 SER 1 
    859 Chain-initial residues that are not actual N termini: 
    860 Chain-final residues that are actual C termini: /A C 18, /B C 18, /C THR 59,
    861 /D LEU 59 
    862 Chain-final residues that are not actual C termini: 
    863 153 hydrogen bonds 
    864 4 hydrogens added 
    865  
    866 
    867 > wait 5
    868 
    869 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--
    870 > WRM-16.result.pdbqt
    871 
    872 Summary of feedback from opening
    873 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--WRM-16.result.pdbqt 
    874 --- 
    875 warnings | Ignored bad PDB record found on line 2 
    876 REMARK VINA RESULT: -7.9 0.000 0.000 
    877  
    878 Ignored bad PDB record found on line 3 
    879 REMARK 5 active torsions: 
    880  
    881 Ignored bad PDB record found on line 4 
    882 REMARK status: ('A' for Active; 'I' for Inactive) 
    883  
    884 Ignored bad PDB record found on line 5 
    885 REMARK 1 A between atoms: C_9 and O_15 
    886  
    887 Ignored bad PDB record found on line 6 
    888 REMARK 2 A between atoms: C_10 and O_17 
    889  
    890 184 messages similar to the above omitted 
    891  
    892 Opened 1D7G--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    893 bonds) 
    894 
    895 > wait 5
    896 
    897 > close #2.2-9
    898 
    899 > wait 5
    900 
    901 > contacts :UNL radius 0.05 log true saveFile
    902 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
    903 > WRM-16.contacts.txt
    904    
    905    
    906     Allowed overlap: -0.4
    907     H-bond overlap reduction: 0.4
    908     Ignore contacts between atoms separated by 4 bonds or less
    909     Detect intra-residue contacts: False
    910     Detect intra-molecule contacts: True
    911    
    912     39 contacts
    913                       atom1                              atom2             overlap  distance
    914     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 HE     0.329    2.431
    915     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 15 1H2'    0.256    2.624
    916     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D LYS 5 HG1    0.119    2.641
    917     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/D ARG 4 2HH1   0.015    2.005
    918     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 NE     -0.009    3.394
    919     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1D7G.pdbqt #1/D LYS 5 CG     -0.009    3.589
    920     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 HB2    -0.018    2.778
    921     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 17 H7      -0.024    2.044
    922     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 16 H7      -0.025    2.045
    923     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1D7G.pdbqt #1/D LYS 5 HG1    -0.045    2.925
    924     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 H7      -0.079    2.959
    925     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/D ARG 4 CZ     -0.085    3.245
    926     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 15 C2'     -0.096    3.676
    927     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1D7G.pdbqt #1/D SER 1 O      -0.112    3.472
    928     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 2HH1   -0.121    2.731
    929     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 HB2    -0.137    2.897
    930     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 N7      -0.144    3.649
    931     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B C 18 H41     -0.162    3.042
    932     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 NH1    -0.162    3.397
    933     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 17 H7      -0.174    2.784
    934     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 15 C8      -0.195    3.315
    935     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D LYS 5 HG1    -0.207    2.817
    936     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/D ARG 4 NH1    -0.209    2.894
    937     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 H7      -0.210    2.820
    938     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 17 C8      -0.227    3.387
    939     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 C8      -0.227    3.807
    940     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D LYS 5 CG     -0.232    3.692
    941     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 N7      -0.234    3.469
    942     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 16 O2P     -0.237    3.197
    943     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 CB     -0.252    3.712
    944     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D LYS 5 N      -0.277    3.662
    945     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 O2P     -0.310    3.570
    946     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 16 H8      -0.331    3.211
    947     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/D ARG 4 NH1    -0.333    2.978
    948     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/B G 15 C8      -0.337    3.647
    949     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C   1D7G.pdbqt #1/D ARG 4 HE     -0.343    2.953
    950     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 16 N7      -0.347    2.992
    951     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 17 N7      -0.366    3.011
    952     1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O   1D7G.pdbqt #1/B G 17 O6      -0.397    3.297
    953    
    954 
    955  
    956 39 contacts 
    957 
    958 > hbonds :UNL showDist true radius 0.05 log true saveFile
    959 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
    960 > WRM-16.hbonds.txt
    961    
    962    
    963     Finding intermodel H-bonds
    964     Finding intramodel H-bonds
    965     Constraints relaxed by 0.4 angstroms and 20 degrees
    966     Models used:
    967         1 1D7G.pdbqt
    968         2.1 1D7G--WRM-16.result.pdbqt
    969    
    970     3 H-bonds
    971     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    972     1D7G.pdbqt #1/B G 16 N7    1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O  1D7G.pdbqt #1/B G 16 H7     2.992  2.045
    973     1D7G.pdbqt #1/B G 17 N7    1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O  1D7G.pdbqt #1/B G 17 H7     3.011  2.044
    974     1D7G.pdbqt #1/D ARG 4 NH1  1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O  1D7G.pdbqt #1/D ARG 4 2HH1  2.978  2.005
    975    
    976 
    977  
    978 3 hydrogen bonds found 
    979 
    980 > select :UNL
    981 
    982 28 atoms, 31 bonds, 1 residue, 1 model selected 
    983 
    984 > label sel text "Ligand "
    985 
    986 > label height 1
    987 
    988 > ~select
    989 
    990 Nothing selected 
    991 
    992 > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
    993 > ypos .95
    994 
    995 > 2dlabels text "1D7G WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    996 
    997 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
    998 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    999 > true
    1000 
    1001 > select :UNL
    1002 
    1003 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1004 
    1005 > view sel
    1006 
    1007 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
    1008 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    1009 > true
    1010 
    1011 > close
    1012 
    1013 > wait 5
    1014 
    1015 > set bgColor white
    1016 
    1017 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1GXC.pdbqt
    1018 
    1019 Chain information for 1GXC.pdbqt #1 
    1020 --- 
    1021 Chain | Description 
    1022 A D G J | No description available 
    1023 B E H K | No description available 
    1024  
    1025 Opened 1GXC.pdbqt containing 1 structures (8116 atoms, 8224 bonds) 
    1026 
    1027 > wait 5
    1028 
    1029 > hide surfaces
    1030 
    1031 > hide atoms
    1032 
    1033 > show cartoons
    1034 
    1035 > wait 5
    1036 
    1037 > addh
    1038 
    1039 Summary of feedback from adding hydrogens to 1GXC.pdbqt #1 
    1040 --- 
    1041 warnings | Not adding hydrogens to /A ASP 111 CB because it is missing heavy-
    1042 atom bond partners 
    1043 Not adding hydrogens to /D ASP 111 CB because it is missing heavy-atom bond
    1044 partners 
    1045 Not adding hydrogens to /G ASP 111 CB because it is missing heavy-atom bond
    1046 partners 
    1047 Not adding hydrogens to /H ARG 7 CB because it is missing heavy-atom bond
    1048 partners 
    1049 Not adding hydrogens to /J ASP 111 CB because it is missing heavy-atom bond
    1050 partners 
    1051 1 messages similar to the above omitted 
    1052 notes | No usable SEQRES records for 1GXC.pdbqt (#1) chain A; guessing termini
    1053 instead 
    1054 No usable SEQRES records for 1GXC.pdbqt (#1) chain B; guessing termini instead 
    1055 No usable SEQRES records for 1GXC.pdbqt (#1) chain D; guessing termini instead 
    1056 No usable SEQRES records for 1GXC.pdbqt (#1) chain E; guessing termini instead 
    1057 No usable SEQRES records for 1GXC.pdbqt (#1) chain G; guessing termini instead 
    1058 3 messages similar to the above omitted 
    1059 Chain-initial residues that are actual N termini: /A PRO 92, /B HIS 0, /D PRO
    1060 92, /E HIS 0, /G PRO 92, /H HIS 0, /J PRO 92, /K HIS 0 
    1061 Chain-initial residues that are not actual N termini: /B TYR 4, /E TYR 4, /H
    1062 TYR 4, /K TYR 4 
    1063 Chain-final residues that are actual C termini: /A ASP 207, /B ARG 7, /D ASP
    1064 207, /E ARG 7, /G ASP 207, /H ARG 7, /J ASP 207, /K ARG 7 
    1065 Chain-final residues that are not actual C termini: /B ASP 2, /E ASP 2, /H ASP
    1066 2, /K ASP 2 
    1067 388 hydrogen bonds 
    1068 Adding 'H' to /B TYR 4 
    1069 Adding 'H' to /E TYR 4 
    1070 Adding 'H' to /H TYR 4 
    1071 Adding 'H' to /K TYR 4 
    1072 /B ASP 2 is not terminus, removing H atom from 'C' 
    1073 /E ASP 2 is not terminus, removing H atom from 'C' 
    1074 /H ASP 2 is not terminus, removing H atom from 'C' 
    1075 /K ASP 2 is not terminus, removing H atom from 'C' 
    1076 0 hydrogens added 
    1077  
    1078 
    1079 > wait 5
    1080 
    1081 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--
    1082 > WRM-16.result.pdbqt
    1083 
    1084 Summary of feedback from opening
    1085 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--WRM-16.result.pdbqt 
    1086 --- 
    1087 warnings | Ignored bad PDB record found on line 2 
    1088 REMARK VINA RESULT: -7.0 0.000 0.000 
    1089  
    1090 Ignored bad PDB record found on line 3 
    1091 REMARK 5 active torsions: 
    1092  
    1093 Ignored bad PDB record found on line 4 
    1094 REMARK status: ('A' for Active; 'I' for Inactive) 
    1095  
    1096 Ignored bad PDB record found on line 5 
    1097 REMARK 1 A between atoms: C_9 and O_15 
    1098  
    1099 Ignored bad PDB record found on line 6 
    1100 REMARK 2 A between atoms: C_10 and O_17 
    1101  
    1102 184 messages similar to the above omitted 
    1103  
    1104 Opened 1GXC--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    1105 bonds) 
    1106 
    1107 > wait 5
    1108 
    1109 > close #2.2-9
    1110 
    1111 > wait 5
    1112 
    1113 > contacts :UNL radius 0.05 log true saveFile
    1114 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
    1115 > WRM-16.contacts.txt
    1116    
    1117    
    1118     Allowed overlap: -0.4
    1119     H-bond overlap reduction: 0.4
    1120     Ignore contacts between atoms separated by 4 bonds or less
    1121     Detect intra-residue contacts: False
    1122     Detect intra-molecule contacts: True
    1123    
    1124     30 contacts
    1125                       atom1                               atom2              overlap  distance
    1126     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 184 HB2    0.193    2.567
    1127     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 HA     0.144    2.736
    1128     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 3HD1   0.103    2.657
    1129     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1GXC.pdbqt #1/D ASN 185 HN     0.074    2.806
    1130     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1GXC.pdbqt #1/D ASN 185 HB2    0.014    2.866
    1131     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 HA     -0.111    2.721
    1132     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1GXC.pdbqt #1/D ASN 185 CB     -0.140    3.720
    1133     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 CA     -0.141    3.721
    1134     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 186 O      -0.141    3.381
    1135     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 3HD1   -0.151    2.761
    1136     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O   1GXC.pdbqt #1/G ARG 132 HD1    -0.159    2.619
    1137     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 185 O      -0.179    3.539
    1138     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 184 CB     -0.181    3.641
    1139     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 185 N      -0.199    3.584
    1140     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 185 HB2    -0.204    2.964
    1141     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O   1GXC.pdbqt #1/G LEU 129 HA     -0.211    2.631
    1142     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 185 O      -0.218    3.458
    1143     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O   1GXC.pdbqt #1/G ARG 132 CD     -0.232    3.392
    1144     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 186 HB1    -0.235    2.995
    1145     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O   1GXC.pdbqt #1/G LEU 129 O      -0.252    3.152
    1146     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/D ASN 185 HN     -0.264    3.024
    1147     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 CD1    -0.264    3.724
    1148     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1GXC.pdbqt #1/D ASN 185 N      -0.278    3.783
    1149     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 3HD1   -0.301    3.061
    1150     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 HB1    -0.310    3.070
    1151     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 N      -0.338    3.843
    1152     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 CD1    -0.354    3.664
    1153     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G ARG 132 HD1    -0.355    3.235
    1154     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O   1GXC.pdbqt #1/D ASN 186 HB2    -0.377    2.837
    1155     1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C   1GXC.pdbqt #1/G LEU 129 CD1    -0.396    3.856
    1156    
    1157 
    1158  
    1159 30 contacts 
    1160 
    1161 > hbonds :UNL showDist true radius 0.05 log true saveFile
    1162 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
    1163 > WRM-16.hbonds.txt
    1164    
    1165    
    1166     Finding intermodel H-bonds
    1167     Finding intramodel H-bonds
    1168     Constraints relaxed by 0.4 angstroms and 20 degrees
    1169     Models used:
    1170         1 1GXC.pdbqt
    1171         2.1 1GXC--WRM-16.result.pdbqt
    1172    
    1173     0 H-bonds
    1174     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    1175    
    1176 
    1177  
    1178 0 hydrogen bonds found 
    1179 
    1180 > select :UNL
    1181 
    1182 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1183 
    1184 > label sel text "Ligand "
    1185 
    1186 > label height 1
    1187 
    1188 > ~select
    1189 
    1190 Nothing selected 
    1191 
    1192 > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
    1193 > ypos .95
    1194 
    1195 > 2dlabels text "1GXC WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    1196 
    1197 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
    1198 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    1199 > true
    1200 
    1201 > select :UNL
    1202 
    1203 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1204 
    1205 > view sel
    1206 
    1207 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
    1208 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    1209 > true
    1210 
    1211 > close
    1212 
    1213 > wait 5
    1214 
    1215 > set bgColor white
    1216 
    1217 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1KO6.pdbqt
    1218 
    1219 Chain information for 1KO6.pdbqt #1 
    1220 --- 
    1221 Chain | Description 
    1222 A | No description available 
    1223 B D | No description available 
    1224 C | No description available 
    1225  
    1226 Opened 1KO6.pdbqt containing 1 structures (4955 atoms, 5004 bonds) 
    1227 
    1228 > wait 5
    1229 
    1230 > hide surfaces
    1231 
    1232 > hide atoms
    1233 
    1234 > show cartoons
    1235 
    1236 > wait 5
    1237 
    1238 > addh
    1239 
    1240 Summary of feedback from adding hydrogens to 1KO6.pdbqt #1 
    1241 --- 
    1242 warnings | Not adding hydrogens to /A MET 712 CB because it is missing heavy-
    1243 atom bond partners 
    1244 Not adding hydrogens to /A LYS 814 CB because it is missing heavy-atom bond
    1245 partners 
    1246 Not adding hydrogens to /C THR 737 CB because it is missing heavy-atom bond
    1247 partners 
    1248 Not adding hydrogens to /D ASP 870 CB because it is missing heavy-atom bond
    1249 partners 
    1250 notes | No usable SEQRES records for 1KO6.pdbqt (#1) chain A; guessing termini
    1251 instead 
    1252 No usable SEQRES records for 1KO6.pdbqt (#1) chain B; guessing termini instead 
    1253 No usable SEQRES records for 1KO6.pdbqt (#1) chain C; guessing termini instead 
    1254 No usable SEQRES records for 1KO6.pdbqt (#1) chain D; guessing termini instead 
    1255 Chain-initial residues that are actual N termini: /A MET 712, /B LYS 865, /C
    1256 HIS 713, /D LYS 865 
    1257 Chain-initial residues that are not actual N termini: /C GLU 742 
    1258 Chain-final residues that are actual C termini: /A PHE 863, /B ASP 870, /C PHE
    1259 863, /D ASP 870 
    1260 Chain-final residues that are not actual C termini: /C ASN 738 
    1261 223 hydrogen bonds 
    1262 Adding 'H' to /C GLU 742 
    1263 /C ASN 738 is not terminus, removing H atom from 'C' 
    1264 1 hydrogens added 
    1265  
    1266 
    1267 > wait 5
    1268 
    1269 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--
    1270 > WRM-16.result.pdbqt
    1271 
    1272 Summary of feedback from opening
    1273 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--WRM-16.result.pdbqt 
    1274 --- 
    1275 warnings | Ignored bad PDB record found on line 2 
    1276 REMARK VINA RESULT: -7.3 0.000 0.000 
    1277  
    1278 Ignored bad PDB record found on line 3 
    1279 REMARK 5 active torsions: 
    1280  
    1281 Ignored bad PDB record found on line 4 
    1282 REMARK status: ('A' for Active; 'I' for Inactive) 
    1283  
    1284 Ignored bad PDB record found on line 5 
    1285 REMARK 1 A between atoms: C_9 and O_15 
    1286  
    1287 Ignored bad PDB record found on line 6 
    1288 REMARK 2 A between atoms: C_10 and O_17 
    1289  
    1290 184 messages similar to the above omitted 
    1291  
    1292 Opened 1KO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    1293 bonds) 
    1294 
    1295 > wait 5
    1296 
    1297 > close #2.2-9
    1298 
    1299 > wait 5
    1300 
    1301 > contacts :UNL radius 0.05 log true saveFile
    1302 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
    1303 > WRM-16.contacts.txt
    1304    
    1305    
    1306     Allowed overlap: -0.4
    1307     H-bond overlap reduction: 0.4
    1308     Ignore contacts between atoms separated by 4 bonds or less
    1309     Detect intra-residue contacts: False
    1310     Detect intra-molecule contacts: True
    1311    
    1312     36 contacts
    1313                      atom1                               atom2              overlap  distance
    1314     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 3HD2   0.149    2.461
    1315     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 3HD2   0.075    2.535
    1316     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 HB2    0.038    2.722
    1317     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 HB2    0.022    2.738
    1318     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 3HD2   -0.109    2.869
    1319     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A VAL 783 2HG1   -0.121    2.731
    1320     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ARG 778 NH2    -0.144    3.649
    1321     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 CD2    -0.149    3.459
    1322     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 CE1    -0.153    3.613
    1323     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 HD1    -0.165    2.925
    1324     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 C      -0.168    3.628
    1325     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/C GLU 848 OE2    -0.172    3.412
    1326     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 HD1    -0.179    2.939
    1327     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ARG 778 CZ     -0.190    3.770
    1328     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ARG 778 CZ     -0.200    3.780
    1329     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O  1KO6.pdbqt #1/A ARG 778 CZ     -0.201    3.361
    1330     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O  1KO6.pdbqt #1/A LEU 786 3HD2   -0.234    2.694
    1331     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 ND1    -0.236    3.621
    1332     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 CD2    -0.243    3.553
    1333     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 HE1    -0.244    3.004
    1334     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 C      -0.255    3.715
    1335     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ARG 778 NE     -0.258    3.763
    1336     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ASP 787 N      -0.265    3.650
    1337     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O  1KO6.pdbqt #1/A ARG 778 CZ     -0.299    3.419
    1338     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 ND1    -0.302    3.687
    1339     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ASP 787 HB2    -0.308    3.068
    1340     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ASP 787 HB2    -0.317    3.077
    1341     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/C ARG 850 HD1    -0.328    3.088
    1342     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/C ARG 850 CD     -0.334    3.794
    1343     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A HIS 776 CE1    -0.338    3.798
    1344     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A ASP 787 CB     -0.340    3.800
    1345     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 CB     -0.345    3.805
    1346     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 O      -0.353    3.593
    1347     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A VAL 783 CG1    -0.358    3.668
    1348     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 CB     -0.362    3.822
    1349     1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C  1KO6.pdbqt #1/A LEU 786 HB2    -0.365    3.125
    1350    
    1351 
    1352  
    1353 36 contacts 
    1354 
    1355 > hbonds :UNL showDist true radius 0.05 log true saveFile
    1356 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
    1357 > WRM-16.hbonds.txt
    1358    
    1359    
    1360     Finding intermodel H-bonds
    1361     Finding intramodel H-bonds
    1362     Constraints relaxed by 0.4 angstroms and 20 degrees
    1363     Models used:
    1364         1 1KO6.pdbqt
    1365         2.1 1KO6--WRM-16.result.pdbqt
    1366    
    1367     0 H-bonds
    1368     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    1369    
    1370 
    1371  
    1372 0 hydrogen bonds found 
    1373 
    1374 > select :UNL
    1375 
    1376 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1377 
    1378 > label sel text "Ligand "
    1379 
    1380 > label height 1
    1381 
    1382 > ~select
    1383 
    1384 Nothing selected 
    1385 
    1386 > 2dlabels text "Binding Energy: -7.3 kcal/mol" color red size 18 xpos .03
    1387 > ypos .95
    1388 
    1389 > 2dlabels text "1KO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    1390 
    1391 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
    1392 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    1393 > true
    1394 
    1395 > select :UNL
    1396 
    1397 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1398 
    1399 > view sel
    1400 
    1401 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
    1402 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    1403 > true
    1404 
    1405 > close
    1406 
    1407 > wait 5
    1408 
    1409 > set bgColor white
    1410 
    1411 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2I2Y.pdbqt
    1412 
    1413 Chain information for 2I2Y.pdbqt #1 
    1414 --- 
    1415 Chain | Description 
    1416 A | No description available 
    1417 B | No description available 
    1418  
    1419 Opened 2I2Y.pdbqt containing 1 structures (2441 atoms, 2472 bonds) 
    1420 
    1421 > wait 5
    1422 
    1423 > hide surfaces
    1424 
    1425 > hide atoms
    1426 
    1427 > show cartoons
    1428 
    1429 > wait 5
    1430 
    1431 > addh
    1432 
    1433 Summary of feedback from adding hydrogens to 2I2Y.pdbqt #1 
    1434 --- 
    1435 notes | No usable SEQRES records for 2I2Y.pdbqt (#1) chain A; guessing termini
    1436 instead 
    1437 No usable SEQRES records for 2I2Y.pdbqt (#1) chain B; guessing termini instead 
    1438 Chain-initial residues that are actual N termini: /A MET 1, /B C 151 
    1439 Chain-initial residues that are not actual N termini: 
    1440 Chain-final residues that are actual C termini: /A ARG 150, /B C 154 
    1441 Chain-final residues that are not actual C termini: 
    1442 171 hydrogen bonds 
    1443 10 hydrogens added 
    1444  
    1445 
    1446 > wait 5
    1447 
    1448 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--
    1449 > WRM-16.result.pdbqt
    1450 
    1451 Summary of feedback from opening
    1452 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--WRM-16.result.pdbqt 
    1453 --- 
    1454 warnings | Ignored bad PDB record found on line 2 
    1455 REMARK VINA RESULT: -6.7 0.000 0.000 
    1456  
    1457 Ignored bad PDB record found on line 3 
    1458 REMARK 5 active torsions: 
    1459  
    1460 Ignored bad PDB record found on line 4 
    1461 REMARK status: ('A' for Active; 'I' for Inactive) 
    1462  
    1463 Ignored bad PDB record found on line 5 
    1464 REMARK 1 A between atoms: C_9 and O_15 
    1465  
    1466 Ignored bad PDB record found on line 6 
    1467 REMARK 2 A between atoms: C_10 and O_17 
    1468  
    1469 184 messages similar to the above omitted 
    1470  
    1471 Opened 2I2Y--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    1472 bonds) 
    1473 
    1474 > wait 5
    1475 
    1476 > close #2.2-9
    1477 
    1478 > wait 5
    1479 
    1480 > contacts :UNL radius 0.05 log true saveFile
    1481 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
    1482 > WRM-16.contacts.txt
    1483    
    1484    
    1485     Allowed overlap: -0.4
    1486     H-bond overlap reduction: 0.4
    1487     Ignore contacts between atoms separated by 4 bonds or less
    1488     Detect intra-residue contacts: False
    1489     Detect intra-molecule contacts: True
    1490    
    1491     42 contacts
    1492                       atom1                               atom2              overlap  distance
    1493     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 O       0.082    3.158
    1494     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 HB3     0.042    2.568
    1495     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD1   0.038    2.722
    1496     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD2   0.018    2.592
    1497     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD2   0.002    2.608
    1498     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD2   -0.056    2.936
    1499     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 HA     -0.087    2.847
    1500     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ARG 128 HG2    -0.102    2.862
    1501     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD1   -0.104    2.864
    1502     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 N      -0.108    3.613
    1503     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 HB3     -0.117    2.877
    1504     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O   2I2Y.pdbqt #1/A ASP 73 O       -0.129    3.029
    1505     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 HA     -0.132    3.012
    1506     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 CD2    -0.137    3.717
    1507     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 CA     -0.151    3.731
    1508     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 HB3    -0.156    2.916
    1509     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 3HD2   -0.160    2.920
    1510     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 OD1     -0.177    3.417
    1511     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 HB3    -0.188    2.798
    1512     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 CB     -0.194    3.504
    1513     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 123 C      -0.215    3.795
    1514     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2I2Y.pdbqt #1/A ARG 150 CZ     -0.217    3.797
    1515     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2I2Y.pdbqt #1/A ARG 150 NH1    -0.264    3.769
    1516     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 CB     -0.268    3.578
    1517     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 HB3     -0.274    3.034
    1518     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 CD1    -0.276    3.736
    1519     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 CB     -0.297    3.877
    1520     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A VAL 127 CG1    -0.301    3.761
    1521     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 CD2    -0.306    3.616
    1522     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A VAL 127 CG1    -0.313    3.773
    1523     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 HB3     -0.320    2.930
    1524     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2I2Y.pdbqt #1/A ARG 150 NH2    -0.323    3.828
    1525     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ARG 128 HG2    -0.332    3.092
    1526     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 68 O       -0.337    3.577
    1527     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ASP 73 CB      -0.338    3.648
    1528     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 123 CB     -0.338    3.918
    1529     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ARG 128 CG     -0.343    3.803
    1530     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O   2I2Y.pdbqt #1/A SER 69 OG      -0.346    2.866
    1531     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 124 CA     -0.358    3.818
    1532     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A SER 69 OG      -0.359    3.469
    1533     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A LEU 144 CD2    -0.367    3.677
    1534     2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C   2I2Y.pdbqt #1/A ALA 123 HB2    -0.389    3.269
    1535    
    1536 
    1537  
    1538 42 contacts 
    1539 
    1540 > hbonds :UNL showDist true radius 0.05 log true saveFile
    1541 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
    1542 > WRM-16.hbonds.txt
    1543    
    1544    
    1545     Finding intermodel H-bonds
    1546     Finding intramodel H-bonds
    1547     Constraints relaxed by 0.4 angstroms and 20 degrees
    1548     Models used:
    1549         1 2I2Y.pdbqt
    1550         2.1 2I2Y--WRM-16.result.pdbqt
    1551    
    1552     0 H-bonds
    1553     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    1554    
    1555 
    1556  
    1557 0 hydrogen bonds found 
    1558 
    1559 > select :UNL
    1560 
    1561 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1562 
    1563 > label sel text "Ligand "
    1564 
    1565 > label height 1
    1566 
    1567 > ~select
    1568 
    1569 Nothing selected 
    1570 
    1571 > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
    1572 > ypos .95
    1573 
    1574 > 2dlabels text "2I2Y WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    1575 
    1576 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
    1577 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    1578 > true
    1579 
    1580 > select :UNL
    1581 
    1582 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1583 
    1584 > view sel
    1585 
    1586 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
    1587 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    1588 > true
    1589 
    1590 > close
    1591 
    1592 > wait 5
    1593 
    1594 > set bgColor white
    1595 
    1596 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CPE.pdbqt
    1597 
    1598 Chain information for 2CPE.pdbqt #1 
    1599 --- 
    1600 Chain | Description 
    1601 A | No description available 
    1602  
    1603 Opened 2CPE.pdbqt containing 1 structures (1663 atoms, 1680 bonds) 
    1604 
    1605 > wait 5
    1606 
    1607 > hide surfaces
    1608 
    1609 > hide atoms
    1610 
    1611 > show cartoons
    1612 
    1613 > wait 5
    1614 
    1615 > addh
    1616 
    1617 Summary of feedback from adding hydrogens to 2CPE.pdbqt #1 
    1618 --- 
    1619 notes | No usable SEQRES records for 2CPE.pdbqt (#1) chain A; guessing termini
    1620 instead 
    1621 Chain-initial residues that are actual N termini: /A GLY 346 
    1622 Chain-initial residues that are not actual N termini: 
    1623 Chain-final residues that are actual C termini: /A GLY 458 
    1624 Chain-final residues that are not actual C termini: 
    1625 43 hydrogen bonds 
    1626 1 hydrogens added 
    1627  
    1628 
    1629 > wait 5
    1630 
    1631 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--
    1632 > WRM-16.result.pdbqt
    1633 
    1634 Summary of feedback from opening
    1635 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--WRM-16.result.pdbqt 
    1636 --- 
    1637 warnings | Ignored bad PDB record found on line 2 
    1638 REMARK VINA RESULT: -6.4 0.000 0.000 
    1639  
    1640 Ignored bad PDB record found on line 3 
    1641 REMARK 5 active torsions: 
    1642  
    1643 Ignored bad PDB record found on line 4 
    1644 REMARK status: ('A' for Active; 'I' for Inactive) 
    1645  
    1646 Ignored bad PDB record found on line 5 
    1647 REMARK 1 A between atoms: C_9 and O_15 
    1648  
    1649 Ignored bad PDB record found on line 6 
    1650 REMARK 2 A between atoms: C_10 and O_17 
    1651  
    1652 184 messages similar to the above omitted 
    1653  
    1654 Opened 2CPE--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    1655 bonds) 
    1656 
    1657 > wait 5
    1658 
    1659 > close #2.2-9
    1660 
    1661 > wait 5
    1662 
    1663 > contacts :UNL radius 0.05 log true saveFile
    1664 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
    1665 > WRM-16.contacts.txt
    1666    
    1667    
    1668     Allowed overlap: -0.4
    1669     H-bond overlap reduction: 0.4
    1670     Ignore contacts between atoms separated by 4 bonds or less
    1671     Detect intra-residue contacts: False
    1672     Detect intra-molecule contacts: True
    1673    
    1674     45 contacts
    1675                       atom1                               atom2              overlap  distance
    1676     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 374 HB2    0.239    2.521
    1677     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CPE.pdbqt #1/A ILE 400 H      0.104    2.776
    1678     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     0.090    2.670
    1679     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A VAL 372 O      0.010    2.930
    1680     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     -0.008    2.768
    1681     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CPE.pdbqt #1/A HIS 399 ND1    -0.011    3.516
    1682     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 O      -0.023    3.263
    1683     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CD1    -0.043    3.503
    1684     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A THR 373 2HG2   -0.051    2.511
    1685     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CPE.pdbqt #1/A HIS 399 CE1    -0.060    3.640
    1686     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 374 CB     -0.065    3.525
    1687     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 2HD1   -0.072    2.832
    1688     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 2HD1   -0.104    2.714
    1689     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A LEU 374 H      -0.106    2.126
    1690     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 2HD2   -0.122    3.002
    1691     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 2HD1   -0.144    2.754
    1692     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 3HD1   -0.145    2.755
    1693     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A VAL 372 O      -0.165    3.525
    1694     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 CD1    -0.165    3.625
    1695     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A GLY 407 O      -0.173    3.413
    1696     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     -0.190    2.800
    1697     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A LEU 402 3HD1   -0.198    2.658
    1698     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CPE.pdbqt #1/A ILE 400 N      -0.226    3.731
    1699     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     -0.233    2.993
    1700     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CB     -0.257    3.717
    1701     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 2HD1   -0.296    3.176
    1702     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 CD1    -0.306    3.766
    1703     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CPE.pdbqt #1/A HIS 399 HA     -0.312    3.192
    1704     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     -0.326    3.086
    1705     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A THR 373 2HG2   -0.326    3.206
    1706     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A THR 373 HA     -0.326    2.746
    1707     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 H      -0.328    2.938
    1708     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A THR 373 HA     -0.343    3.223
    1709     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CB     -0.348    3.808
    1710     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CG1    -0.351    3.811
    1711     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 HB     -0.367    2.977
    1712     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 374 HB2    -0.373    3.133
    1713     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A THR 373 CG2    -0.376    3.536
    1714     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A ASP 370 O      -0.382    3.282
    1715     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 1HD1   -0.384    3.144
    1716     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CPE.pdbqt #1/A LEU 374 N      -0.385    3.030
    1717     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CB     -0.390    3.850
    1718     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A GLY 407 O      -0.392    3.632
    1719     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A ILE 400 CD1    -0.398    3.708
    1720     2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CPE.pdbqt #1/A LEU 402 CD1    -0.400    3.710
    1721    
    1722 
    1723  
    1724 45 contacts 
    1725 
    1726 > hbonds :UNL showDist true radius 0.05 log true saveFile
    1727 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
    1728 > WRM-16.hbonds.txt
    1729    
    1730    
    1731     Finding intermodel H-bonds
    1732     Finding intramodel H-bonds
    1733     Constraints relaxed by 0.4 angstroms and 20 degrees
    1734     Models used:
    1735         1 2CPE.pdbqt
    1736         2.1 2CPE--WRM-16.result.pdbqt
    1737    
    1738     1 H-bonds
    1739     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    1740     2CPE.pdbqt #1/A LEU 374 N  2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O  2CPE.pdbqt #1/A LEU 374 H  3.030  2.126
    1741    
    1742 
    1743  
    1744 1 hydrogen bonds found 
    1745 
    1746 > select :UNL
    1747 
    1748 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1749 
    1750 > label sel text "Ligand "
    1751 
    1752 > label height 1
    1753 
    1754 > ~select
    1755 
    1756 Nothing selected 
    1757 
    1758 > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
    1759 > ypos .95
    1760 
    1761 > 2dlabels text "2CPE WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    1762 
    1763 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
    1764 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    1765 > true
    1766 
    1767 > select :UNL
    1768 
    1769 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1770 
    1771 > view sel
    1772 
    1773 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
    1774 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    1775 > true
    1776 
    1777 > close
    1778 
    1779 > wait 5
    1780 
    1781 > set bgColor white
    1782 
    1783 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XQZ.pdbqt
    1784 
    1785 Chain information for 1XQZ.pdbqt #1 
    1786 --- 
    1787 Chain | Description 
    1788 A | No description available 
    1789  
    1790 Opened 1XQZ.pdbqt containing 1 structures (4460 atoms, 4520 bonds) 
    1791 
    1792 > wait 5
    1793 
    1794 > hide surfaces
    1795 
    1796 > hide atoms
    1797 
    1798 > show cartoons
    1799 
    1800 > wait 5
    1801 
    1802 > addh
    1803 
    1804 Summary of feedback from adding hydrogens to 1XQZ.pdbqt #1 
    1805 --- 
    1806 notes | No usable SEQRES records for 1XQZ.pdbqt (#1) chain A; guessing termini
    1807 instead 
    1808 Chain-initial residues that are actual N termini: /A GLU 32 
    1809 Chain-initial residues that are not actual N termini: 
    1810 Chain-final residues that are actual C termini: /A SER 308 
    1811 Chain-final residues that are not actual C termini: 
    1812 219 hydrogen bonds 
    1813 5 hydrogens added 
    1814  
    1815 
    1816 > wait 5
    1817 
    1818 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--
    1819 > WRM-16.result.pdbqt
    1820 
    1821 Summary of feedback from opening
    1822 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--WRM-16.result.pdbqt 
    1823 --- 
    1824 warnings | Ignored bad PDB record found on line 2 
    1825 REMARK VINA RESULT: -9.1 0.000 0.000 
    1826  
    1827 Ignored bad PDB record found on line 3 
    1828 REMARK 5 active torsions: 
    1829  
    1830 Ignored bad PDB record found on line 4 
    1831 REMARK status: ('A' for Active; 'I' for Inactive) 
    1832  
    1833 Ignored bad PDB record found on line 5 
    1834 REMARK 1 A between atoms: C_9 and O_15 
    1835  
    1836 Ignored bad PDB record found on line 6 
    1837 REMARK 2 A between atoms: C_10 and O_17 
    1838  
    1839 184 messages similar to the above omitted 
    1840  
    1841 Opened 1XQZ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    1842 bonds) 
    1843 
    1844 > wait 5
    1845 
    1846 > close #2.2-9
    1847 
    1848 > wait 5
    1849 
    1850 > contacts :UNL radius 0.05 log true saveFile
    1851 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
    1852 > WRM-16.contacts.txt
    1853    
    1854    
    1855     Allowed overlap: -0.4
    1856     H-bond overlap reduction: 0.4
    1857     Ignore contacts between atoms separated by 4 bonds or less
    1858     Detect intra-residue contacts: False
    1859     Detect intra-molecule contacts: True
    1860    
    1861     84 contacts
    1862                       atom1                               atom2              overlap  distance
    1863     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 3HD1   0.680    2.080
    1864     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 3HD1   0.609    2.151
    1865     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 2HG1   0.394    2.366
    1866     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CD1    0.391    3.069
    1867     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HN     0.374    2.386
    1868     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HB1    0.366    2.514
    1869     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CD1    0.197    3.263
    1870     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A PHE 49 CE1     0.188    3.392
    1871     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 3HG1   0.163    2.597
    1872     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 2HG1   0.161    2.599
    1873     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 N      0.156    3.229
    1874     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LYS 67 HZ3     0.141    2.619
    1875     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A ARG 122 HG1    0.131    2.289
    1876     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 3HD1   0.128    2.752
    1877     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 CG1    0.076    3.384
    1878     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 44 3HD1    0.076    2.684
    1879     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A GLU 121 O      0.067    3.293
    1880     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HN     0.067    2.693
    1881     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 3HD1   0.066    2.694
    1882     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A LEU 174 1HD1   0.058    2.402
    1883     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 CB     0.050    3.530
    1884     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A PHE 49 CZ      0.039    3.541
    1885     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 2HD2   0.018    2.742
    1886     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HN     -0.011    2.771
    1887     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ALA 65 CB      -0.021    3.601
    1888     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HA     -0.021    2.781
    1889     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 CG1    -0.024    3.484
    1890     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CD1    -0.026    3.486
    1891     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 1HG2   -0.033    2.913
    1892     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A ILE 104 1HG2   -0.053    2.513
    1893     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 N      -0.056    3.441
    1894     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 CA     -0.060    3.520
    1895     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 3HG1   -0.062    2.822
    1896     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A PHE 49 CD1     -0.070    3.650
    1897     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CD2    -0.091    3.551
    1898     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 HB     -0.091    2.701
    1899     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 CG1    -0.109    3.569
    1900     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LYS 67 NZ      -0.112    3.497
    1901     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A PHE 49 CE1     -0.120    3.280
    1902     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 CA     -0.125    3.585
    1903     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 HB     -0.127    2.887
    1904     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 174 1HD1   -0.155    3.035
    1905     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 3HD1   -0.155    2.765
    1906     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 HA     -0.161    2.921
    1907     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 CG1    -0.171    3.631
    1908     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 CD1    -0.174    3.634
    1909     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CG2    -0.176    3.636
    1910     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A ARG 122 CG     -0.191    3.311
    1911     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CD1    -0.193    3.773
    1912     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ALA 65 HB3     -0.203    3.083
    1913     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 3HG1   -0.203    2.813
    1914     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A LEU 174 CD1    -0.209    3.369
    1915     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 3HD1   -0.219    2.829
    1916     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LYS 67 HD1     -0.229    2.989
    1917     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 3HD1   -0.241    2.851
    1918     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CB     -0.253    3.713
    1919     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 HB     -0.285    2.895
    1920     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CG2    -0.295    3.605
    1921     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 2HG2   -0.296    2.906
    1922     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1XQZ.pdbqt #1/A VAL 126 O      -0.301    3.661
    1923     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CB     -0.302    3.612
    1924     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 CG     -0.304    3.884
    1925     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 CG2    -0.306    3.886
    1926     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A VAL 52 1HG1    -0.309    2.769
    1927     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ASP 186 N      -0.313    3.698
    1928     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 2HD1   -0.313    3.073
    1929     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ARG 122 HD2    -0.324    3.084
    1930     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 52 1HG1    -0.325    2.935
    1931     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 44 CD1     -0.326    3.786
    1932     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A ILE 185 2HG2   -0.327    2.787
    1933     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 174 1HD2   -0.328    3.208
    1934     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 1HG2   -0.336    3.096
    1935     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CD1    -0.337    3.647
    1936     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A PHE 49 CE2     -0.340    3.920
    1937     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 CG2    -0.342    3.652
    1938     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 2HD1   -0.346    3.106
    1939     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 52 1HG2    -0.351    2.961
    1940     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CG     -0.363    3.823
    1941     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 185 1HG2   -0.366    3.126
    1942     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1XQZ.pdbqt #1/A ILE 185 CG2    -0.373    3.533
    1943     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 CB     -0.387    3.967
    1944     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A LEU 120 HB2    -0.393    3.273
    1945     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A ILE 104 CB     -0.393    3.853
    1946     1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1XQZ.pdbqt #1/A VAL 126 CG2    -0.396    3.856
    1947    
    1948 
    1949  
    1950 84 contacts 
    1951 
    1952 > hbonds :UNL showDist true radius 0.05 log true saveFile
    1953 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
    1954 > WRM-16.hbonds.txt
    1955    
    1956    
    1957     Finding intermodel H-bonds
    1958     Finding intramodel H-bonds
    1959     Constraints relaxed by 0.4 angstroms and 20 degrees
    1960     Models used:
    1961         1 1XQZ.pdbqt
    1962         2.1 1XQZ--WRM-16.result.pdbqt
    1963    
    1964     0 H-bonds
    1965     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    1966    
    1967 
    1968  
    1969 0 hydrogen bonds found 
    1970 
    1971 > select :UNL
    1972 
    1973 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1974 
    1975 > label sel text "Ligand "
    1976 
    1977 > label height 1
    1978 
    1979 > ~select
    1980 
    1981 Nothing selected 
    1982 
    1983 > 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
    1984 > ypos .95
    1985 
    1986 > 2dlabels text "1XQZ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    1987 
    1988 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
    1989 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    1990 > true
    1991 
    1992 > select :UNL
    1993 
    1994 28 atoms, 31 bonds, 1 residue, 1 model selected 
    1995 
    1996 > view sel
    1997 
    1998 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
    1999 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2000 > true
    2001 
    2002 > close
    2003 
    2004 > wait 5
    2005 
    2006 > set bgColor white
    2007 
    2008 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1Z00.pdbqt
    2009 
    2010 Chain information for 1Z00.pdbqt #1 
    2011 --- 
    2012 Chain | Description 
    2013 A | No description available 
    2014 B | No description available 
    2015  
    2016 Opened 1Z00.pdbqt containing 1 structures (2620 atoms, 2640 bonds) 
    2017 
    2018 > wait 5
    2019 
    2020 > hide surfaces
    2021 
    2022 > hide atoms
    2023 
    2024 > show cartoons
    2025 
    2026 > wait 5
    2027 
    2028 > addh
    2029 
    2030 Summary of feedback from adding hydrogens to 1Z00.pdbqt #1 
    2031 --- 
    2032 notes | No usable SEQRES records for 1Z00.pdbqt (#1) chain A; guessing termini
    2033 instead 
    2034 No usable SEQRES records for 1Z00.pdbqt (#1) chain B; guessing termini instead 
    2035 Chain-initial residues that are actual N termini: /A MET 219, /B MET 822 
    2036 Chain-initial residues that are not actual N termini: 
    2037 Chain-final residues that are actual C termini: /A HIS 302, /B LYS 905 
    2038 Chain-final residues that are not actual C termini: 
    2039 131 hydrogen bonds 
    2040 0 hydrogens added 
    2041  
    2042 
    2043 > wait 5
    2044 
    2045 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--
    2046 > WRM-16.result.pdbqt
    2047 
    2048 Summary of feedback from opening
    2049 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--WRM-16.result.pdbqt 
    2050 --- 
    2051 warnings | Ignored bad PDB record found on line 2 
    2052 REMARK VINA RESULT: -6.8 0.000 0.000 
    2053  
    2054 Ignored bad PDB record found on line 3 
    2055 REMARK 5 active torsions: 
    2056  
    2057 Ignored bad PDB record found on line 4 
    2058 REMARK status: ('A' for Active; 'I' for Inactive) 
    2059  
    2060 Ignored bad PDB record found on line 5 
    2061 REMARK 1 A between atoms: C_9 and O_15 
    2062  
    2063 Ignored bad PDB record found on line 6 
    2064 REMARK 2 A between atoms: C_10 and O_17 
    2065  
    2066 184 messages similar to the above omitted 
    2067  
    2068 Opened 1Z00--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    2069 bonds) 
    2070 
    2071 > wait 5
    2072 
    2073 > close #2.2-9
    2074 
    2075 > wait 5
    2076 
    2077 > contacts :UNL radius 0.05 log true saveFile
    2078 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
    2079 > WRM-16.contacts.txt
    2080    
    2081    
    2082     Allowed overlap: -0.4
    2083     H-bond overlap reduction: 0.4
    2084     Ignore contacts between atoms separated by 4 bonds or less
    2085     Detect intra-residue contacts: False
    2086     Detect intra-molecule contacts: True
    2087    
    2088     52 contacts
    2089                       atom1                               atom2              overlap  distance
    2090     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 HB2    0.383    2.377
    2091     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 222 3HD2   0.372    2.388
    2092     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 CB     0.368    3.092
    2093     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 HA     0.193    2.687
    2094     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 O      0.163    3.197
    2095     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HB3    0.104    2.656
    2096     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B GLN 885 HB3    0.064    2.696
    2097     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 CB     0.063    3.397
    2098     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 222 CD2    0.020    3.440
    2099     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 CB     0.011    3.449
    2100     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 CD1    -0.010    3.470
    2101     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 CA     -0.022    3.602
    2102     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 CB     -0.036    3.496
    2103     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HA     -0.039    2.649
    2104     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 HZ3    -0.040    2.800
    2105     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 HZ3    -0.042    2.802
    2106     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HB3    -0.083    2.843
    2107     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/A ASP 230 HB2    -0.087    2.507
    2108     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 HB2    -0.092    2.852
    2109     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 HB2    -0.100    2.860
    2110     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B GLN 885 HB3    -0.122    2.882
    2111     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 3HD1   -0.124    2.884
    2112     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ASP 230 OD2    -0.127    3.367
    2113     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 HB3    -0.147    2.907
    2114     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/A ASP 230 CB     -0.189    3.349
    2115     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 O      -0.208    3.568
    2116     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 CB     -0.211    3.671
    2117     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HA     -0.218    2.828
    2118     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B GLN 885 CD     -0.225    3.685
    2119     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 CB     -0.228    3.688
    2120     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HB1    -0.260    3.020
    2121     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 NZ     -0.264    3.649
    2122     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B GLN 885 CB     -0.269    3.729
    2123     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/B GLN 885 OE1    -0.287    3.227
    2124     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 CD1    -0.288    3.868
    2125     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 HB3    -0.291    3.051
    2126     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1Z00.pdbqt #1/A LEU 222 CD2    -0.295    3.875
    2127     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 CB     -0.302    3.762
    2128     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A MET 219 O      -0.310    3.400
    2129     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HB3    -0.324    3.084
    2130     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 HA     -0.326    3.086
    2131     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/A ASP 230 CG     -0.329    3.489
    2132     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 NZ     -0.336    3.721
    2133     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LEU 227 N      -0.340    3.845
    2134     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ALA 220 CA     -0.348    3.658
    2135     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/A ASP 230 HB3    -0.357    2.817
    2136     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B GLN 885 CB     -0.359    3.819
    2137     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/B PRO 845 CB     -0.362    3.822
    2138     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A LYS 226 CB     -0.369    3.829
    2139     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ASP 230 OD2    -0.371    3.461
    2140     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C   1Z00.pdbqt #1/A ASP 230 OD2    -0.380    3.470
    2141     1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O   1Z00.pdbqt #1/A ASP 230 CB     -0.386    3.506
    2142    
    2143 
    2144  
    2145 52 contacts 
    2146 
    2147 > hbonds :UNL showDist true radius 0.05 log true saveFile
    2148 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
    2149 > WRM-16.hbonds.txt
    2150    
    2151    
    2152     Finding intermodel H-bonds
    2153     Finding intramodel H-bonds
    2154     Constraints relaxed by 0.4 angstroms and 20 degrees
    2155     Models used:
    2156         1 1Z00.pdbqt
    2157         2.1 1Z00--WRM-16.result.pdbqt
    2158    
    2159     0 H-bonds
    2160     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    2161    
    2162 
    2163  
    2164 0 hydrogen bonds found 
    2165 
    2166 > select :UNL
    2167 
    2168 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2169 
    2170 > label sel text "Ligand "
    2171 
    2172 > label height 1
    2173 
    2174 > ~select
    2175 
    2176 Nothing selected 
    2177 
    2178 > 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
    2179 > ypos .95
    2180 
    2181 > 2dlabels text "1Z00 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    2182 
    2183 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
    2184 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    2185 > true
    2186 
    2187 > select :UNL
    2188 
    2189 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2190 
    2191 > view sel
    2192 
    2193 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
    2194 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2195 > true
    2196 
    2197 > close
    2198 
    2199 > wait 5
    2200 
    2201 > set bgColor white
    2202 
    2203 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2N1I.pdbqt
    2204 
    2205 Chain information for 2N1I.pdbqt #1 
    2206 --- 
    2207 Chain | Description 
    2208 A | No description available 
    2209  
    2210 Opened 2N1I.pdbqt containing 1 structures (2650 atoms, 2682 bonds) 
    2211 
    2212 > wait 5
    2213 
    2214 > hide surfaces
    2215 
    2216 > hide atoms
    2217 
    2218 > show cartoons
    2219 
    2220 > wait 5
    2221 
    2222 > addh
    2223 
    2224 Summary of feedback from adding hydrogens to 2N1I.pdbqt #1 
    2225 --- 
    2226 notes | No usable SEQRES records for 2N1I.pdbqt (#1) chain A; guessing termini
    2227 instead 
    2228 Chain-initial residues that are actual N termini: /A GLY 51 
    2229 Chain-initial residues that are not actual N termini: 
    2230 Chain-final residues that are actual C termini: /A GLU 226 
    2231 Chain-final residues that are not actual C termini: 
    2232 70 hydrogen bonds 
    2233 0 hydrogens added 
    2234  
    2235 
    2236 > wait 5
    2237 
    2238 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--
    2239 > WRM-16.result.pdbqt
    2240 
    2241 Summary of feedback from opening
    2242 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--WRM-16.result.pdbqt 
    2243 --- 
    2244 warnings | Ignored bad PDB record found on line 2 
    2245 REMARK VINA RESULT: -6.7 0.000 0.000 
    2246  
    2247 Ignored bad PDB record found on line 3 
    2248 REMARK 5 active torsions: 
    2249  
    2250 Ignored bad PDB record found on line 4 
    2251 REMARK status: ('A' for Active; 'I' for Inactive) 
    2252  
    2253 Ignored bad PDB record found on line 5 
    2254 REMARK 1 A between atoms: C_9 and O_15 
    2255  
    2256 Ignored bad PDB record found on line 6 
    2257 REMARK 2 A between atoms: C_10 and O_17 
    2258  
    2259 184 messages similar to the above omitted 
    2260  
    2261 Opened 2N1I--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    2262 bonds) 
    2263 
    2264 > wait 5
    2265 
    2266 > close #2.2-9
    2267 
    2268 > wait 5
    2269 
    2270 > contacts :UNL radius 0.05 log true saveFile
    2271 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
    2272 > WRM-16.contacts.txt
    2273    
    2274    
    2275     Allowed overlap: -0.4
    2276     H-bond overlap reduction: 0.4
    2277     Ignore contacts between atoms separated by 4 bonds or less
    2278     Detect intra-residue contacts: False
    2279     Detect intra-molecule contacts: True
    2280    
    2281     54 contacts
    2282                       atom1                               atom2              overlap  distance
    2283     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 109 H      0.318    2.562
    2284     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    0.108    2.652
    2285     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 159 HB3    0.091    2.789
    2286     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 3HG1   0.063    2.547
    2287     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A LYS 103 O      0.016    3.344
    2288     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    0.000    2.760
    2289     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 3HG1   -0.025    2.635
    2290     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 109 N      -0.031    3.536
    2291     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 HA     -0.034    2.794
    2292     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 3HG1   -0.037    2.797
    2293     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A ARG 102 NH2    -0.075    3.580
    2294     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 CB     -0.088    3.548
    2295     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 159 H      -0.095    2.975
    2296     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 102 NH1    -0.100    3.605
    2297     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 159 O      -0.123    3.483
    2298     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 102 2HH1   -0.129    3.009
    2299     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 HB2    -0.146    2.756
    2300     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 83 OD1     -0.153    3.513
    2301     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 159 CB     -0.155    3.735
    2302     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    -0.170    2.780
    2303     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A LYS 103 HE2    -0.171    3.051
    2304     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 HB3    -0.175    2.935
    2305     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 CG     -0.213    3.673
    2306     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 CG1    -0.216    3.526
    2307     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A ARG 102 CZ     -0.232    3.812
    2308     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 HA     -0.236    3.116
    2309     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    -0.246    3.006
    2310     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 105 H      -0.256    3.016
    2311     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 102 NH1    -0.256    3.641
    2312     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 159 N      -0.266    3.771
    2313     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A ASP 159 O      -0.268    3.208
    2314     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 109 O      -0.271    3.631
    2315     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 CA     -0.275    3.855
    2316     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HA     -0.288    3.048
    2317     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A CYS 157 O      -0.304    3.544
    2318     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 CG1    -0.306    3.616
    2319     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 HB2    -0.307    3.187
    2320     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A MET 104 SD     -0.309    3.511
    2321     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A ASP 159 H      -0.310    2.370
    2322     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 CB     -0.311    3.891
    2323     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A MET 104 HA     -0.317    3.197
    2324     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 CG1    -0.327    3.787
    2325     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2N1I.pdbqt #1/A LYS 103 CE     -0.328    3.908
    2326     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 CG     -0.330    3.790
    2327     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A VAL 158 CA     -0.338    3.798
    2328     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    -0.339    3.099
    2329     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ARG 109 NH1    -0.340    3.845
    2330     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HG2    -0.369    2.979
    2331     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A GLU 108 CB     -0.369    3.679
    2332     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A VAL 158 CG1    -0.385    3.545
    2333     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A ASP 159 C      -0.387    3.547
    2334     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A MET 104 HA     -0.391    3.001
    2335     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C   2N1I.pdbqt #1/A ASP 83 OD2     -0.395    3.635
    2336     2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O   2N1I.pdbqt #1/A ARG 109 O      -0.398    3.298
    2337    
    2338 
    2339  
    2340 54 contacts 
    2341 
    2342 > hbonds :UNL showDist true radius 0.05 log true saveFile
    2343 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
    2344 > WRM-16.hbonds.txt
    2345    
    2346    
    2347     Finding intermodel H-bonds
    2348     Finding intramodel H-bonds
    2349     Constraints relaxed by 0.4 angstroms and 20 degrees
    2350     Models used:
    2351         1 2N1I.pdbqt
    2352         2.1 2N1I--WRM-16.result.pdbqt
    2353    
    2354     1 H-bonds
    2355     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    2356     2N1I.pdbqt #1/A ASP 159 N  2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O  2N1I.pdbqt #1/A ASP 159 H  3.116  2.370
    2357    
    2358 
    2359  
    2360 1 hydrogen bonds found 
    2361 
    2362 > select :UNL
    2363 
    2364 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2365 
    2366 > label sel text "Ligand "
    2367 
    2368 > label height 1
    2369 
    2370 > ~select
    2371 
    2372 Nothing selected 
    2373 
    2374 > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
    2375 > ypos .95
    2376 
    2377 > 2dlabels text "2N1I WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    2378 
    2379 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
    2380 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    2381 > true
    2382 
    2383 > select :UNL
    2384 
    2385 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2386 
    2387 > view sel
    2388 
    2389 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
    2390 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2391 > true
    2392 
    2393 > close
    2394 
    2395 > wait 5
    2396 
    2397 > set bgColor white
    2398 
    2399 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1P4U.pdbqt
    2400 
    2401 Chain information for 1P4U.pdbqt #1 
    2402 --- 
    2403 Chain | Description 
    2404 A | No description available 
    2405 B | No description available 
    2406  
    2407 Opened 1P4U.pdbqt containing 1 structures (2389 atoms, 2419 bonds) 
    2408 
    2409 > wait 5
    2410 
    2411 > hide surfaces
    2412 
    2413 > hide atoms
    2414 
    2415 > show cartoons
    2416 
    2417 > wait 5
    2418 
    2419 > addh
    2420 
    2421 Summary of feedback from adding hydrogens to 1P4U.pdbqt #1 
    2422 --- 
    2423 notes | No usable SEQRES records for 1P4U.pdbqt (#1) chain A; guessing termini
    2424 instead 
    2425 No usable SEQRES records for 1P4U.pdbqt (#1) chain B; guessing termini instead 
    2426 Chain-initial residues that are actual N termini: /A LEU 579, /B ASP -1 
    2427 Chain-initial residues that are not actual N termini: 
    2428 Chain-final residues that are actual C termini: /A LEU 723, /B ALA 6 
    2429 Chain-final residues that are not actual C termini: 
    2430 95 hydrogen bonds 
    2431 1 hydrogens added 
    2432  
    2433 
    2434 > wait 5
    2435 
    2436 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--
    2437 > WRM-16.result.pdbqt
    2438 
    2439 Summary of feedback from opening
    2440 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--WRM-16.result.pdbqt 
    2441 --- 
    2442 warnings | Ignored bad PDB record found on line 2 
    2443 REMARK VINA RESULT: -7.2 0.000 0.000 
    2444  
    2445 Ignored bad PDB record found on line 3 
    2446 REMARK 5 active torsions: 
    2447  
    2448 Ignored bad PDB record found on line 4 
    2449 REMARK status: ('A' for Active; 'I' for Inactive) 
    2450  
    2451 Ignored bad PDB record found on line 5 
    2452 REMARK 1 A between atoms: C_9 and O_15 
    2453  
    2454 Ignored bad PDB record found on line 6 
    2455 REMARK 2 A between atoms: C_10 and O_17 
    2456  
    2457 184 messages similar to the above omitted 
    2458  
    2459 Opened 1P4U--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    2460 bonds) 
    2461 
    2462 > wait 5
    2463 
    2464 > close #2.2-9
    2465 
    2466 > wait 5
    2467 
    2468 > contacts :UNL radius 0.05 log true saveFile
    2469 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
    2470 > WRM-16.contacts.txt
    2471    
    2472    
    2473     Allowed overlap: -0.4
    2474     H-bond overlap reduction: 0.4
    2475     Ignore contacts between atoms separated by 4 bonds or less
    2476     Detect intra-residue contacts: False
    2477     Detect intra-molecule contacts: True
    2478    
    2479     55 contacts
    2480                       atom1                               atom2              overlap  distance
    2481     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A THR 677 2HG2   0.351    2.409
    2482     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A PRO 593 HA     0.208    2.212
    2483     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A ALA 614 HA     0.167    2.253
    2484     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PHE 613 O      0.103    3.257
    2485     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A ILE 591 HB     0.100    2.320
    2486     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A VAL 628 3HG2   0.090    2.790
    2487     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD1   0.056    2.704
    2488     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PRO 593 HA     0.043    2.567
    2489     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A THR 677 CG2    0.014    3.446
    2490     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD2   -0.042    2.652
    2491     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A VAL 628 2HG1   -0.044    2.804
    2492     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A VAL 628 3HG2   -0.081    2.501
    2493     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A VAL 628 CG2    -0.090    3.670
    2494     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PHE 613 N      -0.098    3.603
    2495     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A SER 594 OG     -0.119    3.499
    2496     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HD1    -0.120    2.730
    2497     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HB1    -0.124    3.004
    2498     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD2   -0.157    2.917
    2499     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A PRO 593 CA     -0.173    3.293
    2500     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HB1    -0.186    2.796
    2501     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A ALA 614 CA     -0.187    3.307
    2502     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HD1    -0.198    2.808
    2503     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 ND1    -0.204    3.439
    2504     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A VAL 628 CG2    -0.210    3.370
    2505     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A VAL 628 3HG2   -0.214    2.674
    2506     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A ILE 591 CB     -0.242    3.362
    2507     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A PHE 613 O      -0.248    3.148
    2508     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A ALA 596 O      -0.255    3.615
    2509     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 CD2    -0.257    3.717
    2510     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HD1    -0.261    3.021
    2511     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 HG     -0.270    3.030
    2512     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD2   -0.273    3.033
    2513     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 ND1    -0.277    3.782
    2514     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A LYS 592 O      -0.287    3.187
    2515     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 CB     -0.297    3.877
    2516     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 CE1    -0.299    3.879
    2517     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 CD1    -0.303    3.763
    2518     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A VAL 628 3HG2   -0.306    2.916
    2519     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD1   -0.312    2.922
    2520     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A SER 594 HN     -0.324    3.204
    2521     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1P4U.pdbqt #1/A LEU 588 1HD2   -0.333    3.213
    2522     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PRO 593 CA     -0.342    3.652
    2523     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PHE 613 HN     -0.343    3.223
    2524     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A SER 594 HN     -0.343    2.403
    2525     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 ND1    -0.350    3.735
    2526     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 HB1    -0.352    2.962
    2527     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O   1P4U.pdbqt #1/A ILE 591 CG2    -0.367    3.527
    2528     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PRO 593 HA     -0.370    2.980
    2529     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 CA     -0.376    3.956
    2530     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 1HD1   -0.379    3.139
    2531     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 ND1    -0.389    3.624
    2532     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A HIS 612 C      -0.391    3.971
    2533     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 CG     -0.391    3.851
    2534     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A LEU 588 CD2    -0.395    3.705
    2535     1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C   1P4U.pdbqt #1/A PRO 593 HB2    -0.395    3.005
    2536    
    2537 
    2538  
    2539 55 contacts 
    2540 
    2541 > hbonds :UNL showDist true radius 0.05 log true saveFile
    2542 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
    2543 > WRM-16.hbonds.txt
    2544    
    2545    
    2546     Finding intermodel H-bonds
    2547     Finding intramodel H-bonds
    2548     Constraints relaxed by 0.4 angstroms and 20 degrees
    2549     Models used:
    2550         1 1P4U.pdbqt
    2551         2.1 1P4U--WRM-16.result.pdbqt
    2552    
    2553     1 H-bonds
    2554     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    2555     1P4U.pdbqt #1/A SER 594 N  1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O  1P4U.pdbqt #1/A SER 594 HN  3.335  2.403
    2556    
    2557 
    2558  
    2559 1 hydrogen bonds found 
    2560 
    2561 > select :UNL
    2562 
    2563 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2564 
    2565 > label sel text "Ligand "
    2566 
    2567 > label height 1
    2568 
    2569 > ~select
    2570 
    2571 Nothing selected 
    2572 
    2573 > 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
    2574 > ypos .95
    2575 
    2576 > 2dlabels text "1P4U WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    2577 
    2578 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
    2579 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    2580 > true
    2581 
    2582 > select :UNL
    2583 
    2584 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2585 
    2586 > view sel
    2587 
    2588 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
    2589 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2590 > true
    2591 
    2592 > close
    2593 
    2594 > wait 5
    2595 
    2596 > set bgColor white
    2597 
    2598 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KCX.pdbqt
    2599 
    2600 Chain information for 2KCX.pdbqt #1 
    2601 --- 
    2602 Chain | Description 
    2603 A | No description available 
    2604  
    2605 Opened 2KCX.pdbqt containing 1 structures (1066 atoms, 1073 bonds) 
    2606 
    2607 > wait 5
    2608 
    2609 > hide surfaces
    2610 
    2611 > hide atoms
    2612 
    2613 > show cartoons
    2614 
    2615 > wait 5
    2616 
    2617 > addh
    2618 
    2619 Summary of feedback from adding hydrogens to 2KCX.pdbqt #1 
    2620 --- 
    2621 notes | No usable SEQRES records for 2KCX.pdbqt (#1) chain A; guessing termini
    2622 instead 
    2623 Chain-initial residues that are actual N termini: /A SER 1 
    2624 Chain-initial residues that are not actual N termini: 
    2625 Chain-final residues that are actual C termini: /A LYS 74 
    2626 Chain-final residues that are not actual C termini: 
    2627 56 hydrogen bonds 
    2628 10 hydrogens added 
    2629  
    2630 
    2631 > wait 5
    2632 
    2633 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--
    2634 > WRM-16.result.pdbqt
    2635 
    2636 Summary of feedback from opening
    2637 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--WRM-16.result.pdbqt 
    2638 --- 
    2639 warnings | Ignored bad PDB record found on line 2 
    2640 REMARK VINA RESULT: -6.4 0.000 0.000 
    2641  
    2642 Ignored bad PDB record found on line 3 
    2643 REMARK 5 active torsions: 
    2644  
    2645 Ignored bad PDB record found on line 4 
    2646 REMARK status: ('A' for Active; 'I' for Inactive) 
    2647  
    2648 Ignored bad PDB record found on line 5 
    2649 REMARK 1 A between atoms: C_9 and O_15 
    2650  
    2651 Ignored bad PDB record found on line 6 
    2652 REMARK 2 A between atoms: C_10 and O_17 
    2653  
    2654 184 messages similar to the above omitted 
    2655  
    2656 Opened 2KCX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    2657 bonds) 
    2658 
    2659 > wait 5
    2660 
    2661 > close #2.2-9
    2662 
    2663 > wait 5
    2664 
    2665 > contacts :UNL radius 0.05 log true saveFile
    2666 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
    2667 > WRM-16.contacts.txt
    2668    
    2669    
    2670     Allowed overlap: -0.4
    2671     H-bond overlap reduction: 0.4
    2672     Ignore contacts between atoms separated by 4 bonds or less
    2673     Detect intra-residue contacts: False
    2674     Detect intra-molecule contacts: True
    2675    
    2676     41 contacts
    2677                       atom1                              atom2             overlap  distance
    2678     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A HIS 61 HE2   0.106    2.504
    2679     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 HG3   0.085    2.675
    2680     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 HG3   0.014    2.596
    2681     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 HG3   0.013    2.747
    2682     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A PRO 28 HD3   0.006    2.874
    2683     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KCX.pdbqt #1/A HIS 61 HE2   -0.031    2.091
    2684     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 CE2   -0.034    3.344
    2685     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A ALA 55 HB2   -0.081    2.961
    2686     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 HG3   -0.125    2.885
    2687     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 HA    -0.126    2.886
    2688     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A ALA 55 CB    -0.136    3.716
    2689     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 45 CB    -0.155    3.615
    2690     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A HIS 61 NE2   -0.167    3.402
    2691     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 CA    -0.168    3.628
    2692     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A PRO 28 CD    -0.169    3.749
    2693     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 CG    -0.185    3.645
    2694     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 HG3   -0.195    2.955
    2695     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A PRO 28 CG    -0.207    3.787
    2696     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 45 CB    -0.220    3.800
    2697     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 HA    -0.222    2.982
    2698     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A HIS 61 HE2   -0.225    3.105
    2699     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 55 CB    -0.229    3.689
    2700     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 HA    -0.239    2.999
    2701     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A HIS 61 HE2   -0.246    3.126
    2702     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 CE2   -0.247    3.557
    2703     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KCX.pdbqt #1/A PRO 28 HG3   -0.250    3.130
    2704     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 CG    -0.250    3.560
    2705     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 45 HB1   -0.258    3.018
    2706     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ARG 59 CG    -0.260    3.720
    2707     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A HIS 61 NE2   -0.261    3.766
    2708     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A GLU 52 OE1   -0.267    3.507
    2709     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A THR 46 O     -0.276    3.516
    2710     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 CE2   -0.276    3.736
    2711     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 CE2   -0.281    3.591
    2712     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 CB    -0.323    3.783
    2713     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A TYR 47 CD2   -0.340    3.800
    2714     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 N     -0.347    3.732
    2715     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 CB    -0.361    3.941
    2716     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 56 HB2   -0.382    3.142
    2717     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KCX.pdbqt #1/A HIS 61 NE2   -0.387    3.072
    2718     2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KCX.pdbqt #1/A ALA 55 HB3   -0.388    3.148
    2719    
    2720 
    2721  
    2722 41 contacts 
    2723 
    2724 > hbonds :UNL showDist true radius 0.05 log true saveFile
    2725 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
    2726 > WRM-16.hbonds.txt
    2727    
    2728    
    2729     Finding intermodel H-bonds
    2730     Finding intramodel H-bonds
    2731     Constraints relaxed by 0.4 angstroms and 20 degrees
    2732     Models used:
    2733         1 2KCX.pdbqt
    2734         2.1 2KCX--WRM-16.result.pdbqt
    2735    
    2736     1 H-bonds
    2737     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    2738     2KCX.pdbqt #1/A HIS 61 NE2  2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O  2KCX.pdbqt #1/A HIS 61 HE2  3.072  2.091
    2739    
    2740 
    2741  
    2742 1 hydrogen bonds found 
    2743 
    2744 > select :UNL
    2745 
    2746 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2747 
    2748 > label sel text "Ligand "
    2749 
    2750 > label height 1
    2751 
    2752 > ~select
    2753 
    2754 Nothing selected 
    2755 
    2756 > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
    2757 > ypos .95
    2758 
    2759 > 2dlabels text "2KCX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    2760 
    2761 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
    2762 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    2763 > true
    2764 
    2765 > select :UNL
    2766 
    2767 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2768 
    2769 > view sel
    2770 
    2771 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
    2772 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2773 > true
    2774 
    2775 > close
    2776 
    2777 > wait 5
    2778 
    2779 > set bgColor white
    2780 
    2781 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1VR2.pdbqt
    2782 
    2783 Chain information for 1VR2.pdbqt #1 
    2784 --- 
    2785 Chain | Description 
    2786 A | No description available 
    2787  
    2788 Opened 1VR2.pdbqt containing 1 structures (4310 atoms, 4361 bonds) 
    2789 
    2790 > wait 5
    2791 
    2792 > hide surfaces
    2793 
    2794 > hide atoms
    2795 
    2796 > show cartoons
    2797 
    2798 > wait 5
    2799 
    2800 > addh
    2801 
    2802 Summary of feedback from adding hydrogens to 1VR2.pdbqt #1 
    2803 --- 
    2804 warnings | Not adding hydrogens to /A LYS 838 CB because it is missing heavy-
    2805 atom bond partners 
    2806 Not adding hydrogens to /A ARG 842 CB because it is missing heavy-atom bond
    2807 partners 
    2808 Not adding hydrogens to /A PHE 845 CB because it is missing heavy-atom bond
    2809 partners 
    2810 Not adding hydrogens to /A TYR 938 CB because it is missing heavy-atom bond
    2811 partners 
    2812 Not adding hydrogens to /A LYS 939 CB because it is missing heavy-atom bond
    2813 partners 
    2814 6 messages similar to the above omitted 
    2815 notes | No usable SEQRES records for 1VR2.pdbqt (#1) chain A; guessing termini
    2816 instead 
    2817 Chain-initial residues that are actual N termini: /A LEU 820 
    2818 Chain-initial residues that are not actual N termini: /A ASP 998, /A ASP 1064 
    2819 Chain-final residues that are actual C termini: /A ALA 1168 
    2820 Chain-final residues that are not actual C termini: /A LYS 939, /A PHE 1047 
    2821 222 hydrogen bonds 
    2822 Adding 'H' to /A ASP 998 
    2823 Adding 'H' to /A ASP 1064 
    2824 /A LYS 939 is not terminus, removing H atom from 'C' 
    2825 /A PHE 1047 is not terminus, removing H atom from 'C' 
    2826 2 hydrogens added 
    2827  
    2828 
    2829 > wait 5
    2830 
    2831 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--
    2832 > WRM-16.result.pdbqt
    2833 
    2834 Summary of feedback from opening
    2835 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--WRM-16.result.pdbqt 
    2836 --- 
    2837 warnings | Ignored bad PDB record found on line 2 
    2838 REMARK VINA RESULT: -7.7 0.000 0.000 
    2839  
    2840 Ignored bad PDB record found on line 3 
    2841 REMARK 5 active torsions: 
    2842  
    2843 Ignored bad PDB record found on line 4 
    2844 REMARK status: ('A' for Active; 'I' for Inactive) 
    2845  
    2846 Ignored bad PDB record found on line 5 
    2847 REMARK 1 A between atoms: C_9 and O_15 
    2848  
    2849 Ignored bad PDB record found on line 6 
    2850 REMARK 2 A between atoms: C_10 and O_17 
    2851  
    2852 184 messages similar to the above omitted 
    2853  
    2854 Opened 1VR2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    2855 bonds) 
    2856 
    2857 > wait 5
    2858 
    2859 > close #2.2-9
    2860 
    2861 > wait 5
    2862 
    2863 > contacts :UNL radius 0.05 log true saveFile
    2864 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
    2865 > WRM-16.contacts.txt
    2866    
    2867    
    2868     Allowed overlap: -0.4
    2869     H-bond overlap reduction: 0.4
    2870     Ignore contacts between atoms separated by 4 bonds or less
    2871     Detect intra-residue contacts: False
    2872     Detect intra-molecule contacts: True
    2873    
    2874     47 contacts
    2875                       atom1                               atom2              overlap  distance
    2876     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A GLY 846 HA1    0.221    2.659
    2877     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A LYS 868 HB1    0.195    2.685
    2878     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A CYS 919 HN     0.178    2.582
    2879     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 3HG2   0.116    2.764
    2880     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A CYS 919 HN     0.070    2.690
    2881     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A GLN 847 HN     0.070    2.810
    2882     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 CG2    0.032    3.548
    2883     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O   1VR2.pdbqt #1/A VAL 848 3HG2   0.032    2.428
    2884     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A ALA 866 HB3    -0.025    2.785
    2885     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A LYS 868 CB     -0.077    3.657
    2886     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A ALA 866 CB     -0.081    3.541
    2887     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A GLY 846 CA     -0.093    3.673
    2888     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 2HD1   -0.095    2.855
    2889     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A ALA 866 CB     -0.107    3.567
    2890     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1VR2.pdbqt #1/A GLN 847 N      -0.119    3.624
    2891     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 HE1    -0.150    2.910
    2892     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A PHE 918 CD1    -0.161    3.621
    2893     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A PHE 918 HA     -0.164    2.924
    2894     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A CYS 919 N      -0.209    3.594
    2895     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A GLN 847 N      -0.223    3.608
    2896     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 HG2    -0.224    2.984
    2897     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A CYS 919 N      -0.239    3.624
    2898     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O   1VR2.pdbqt #1/A LEU 840 O      -0.244    3.184
    2899     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O   1VR2.pdbqt #1/A VAL 848 2HG1   -0.254    2.714
    2900     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A CYS 919 O      -0.260    3.500
    2901     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 CG2    -0.269    3.729
    2902     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 CG2    -0.280    3.740
    2903     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 3HG2   -0.284    2.894
    2904     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 CE     -0.291    3.751
    2905     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 2HG1   -0.295    2.905
    2906     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 CG     -0.303    3.763
    2907     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 2HD1   -0.308    3.068
    2908     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 2HD1   -0.310    3.070
    2909     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O   1VR2.pdbqt #1/A VAL 848 CG2    -0.320    3.480
    2910     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 HB2    -0.324    2.934
    2911     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A PHE 918 CE1    -0.326    3.786
    2912     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 HE1    -0.332    3.092
    2913     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 CG2    -0.343    3.803
    2914     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 CG2    -0.351    3.811
    2915     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 3HG2   -0.354    2.964
    2916     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 1HG2   -0.357    3.117
    2917     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 1HG2   -0.371    3.131
    2918     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A ALA 866 HB1    -0.375    3.135
    2919     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A VAL 848 2HG2   -0.383    3.143
    2920     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 HB2    -0.387    2.997
    2921     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LYS 868 CD     -0.393    3.853
    2922     1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C   1VR2.pdbqt #1/A LEU 840 HB2    -0.399    3.159
    2923    
    2924 
    2925  
    2926 47 contacts 
    2927 
    2928 > hbonds :UNL showDist true radius 0.05 log true saveFile
    2929 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
    2930 > WRM-16.hbonds.txt
    2931    
    2932    
    2933     Finding intermodel H-bonds
    2934     Finding intramodel H-bonds
    2935     Constraints relaxed by 0.4 angstroms and 20 degrees
    2936     Models used:
    2937         1 1VR2.pdbqt
    2938         2.1 1VR2--WRM-16.result.pdbqt
    2939    
    2940     0 H-bonds
    2941     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    2942    
    2943 
    2944  
    2945 0 hydrogen bonds found 
    2946 
    2947 > select :UNL
    2948 
    2949 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2950 
    2951 > label sel text "Ligand "
    2952 
    2953 > label height 1
    2954 
    2955 > ~select
    2956 
    2957 Nothing selected 
    2958 
    2959 > 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
    2960 > ypos .95
    2961 
    2962 > 2dlabels text "1VR2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    2963 
    2964 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
    2965 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    2966 > true
    2967 
    2968 > select :UNL
    2969 
    2970 28 atoms, 31 bonds, 1 residue, 1 model selected 
    2971 
    2972 > view sel
    2973 
    2974 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
    2975 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    2976 > true
    2977 
    2978 > close
    2979 
    2980 > wait 5
    2981 
    2982 > set bgColor white
    2983 
    2984 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5AX3.pdbqt
    2985 
    2986 Chain information for 5AX3.pdbqt #1 
    2987 --- 
    2988 Chain | Description 
    2989 A | No description available 
    2990 B | No description available 
    2991  
    2992 Opened 5AX3.pdbqt containing 1 structures (5669 atoms, 5733 bonds) 
    2993 
    2994 > wait 5
    2995 
    2996 > hide surfaces
    2997 
    2998 > hide atoms
    2999 
    3000 > show cartoons
    3001 
    3002 > wait 5
    3003 
    3004 > addh
    3005 
    3006 Summary of feedback from adding hydrogens to 5AX3.pdbqt #1 
    3007 --- 
    3008 notes | No usable SEQRES records for 5AX3.pdbqt (#1) chain A; guessing termini
    3009 instead 
    3010 No usable SEQRES records for 5AX3.pdbqt (#1) chain B; guessing termini instead 
    3011 Chain-initial residues that are actual N termini: /A GLY 1, /B LEU 349 
    3012 Chain-initial residues that are not actual N termini: /A TYR 27, /A PHE 174,
    3013 /A THR 181, /A GLY 194, /A LEU 248 
    3014 Chain-final residues that are actual C termini: /A TYR 348, /B GLU 360 
    3015 Chain-final residues that are not actual C termini: /A GLU 24, /A ALA 165, /A
    3016 VAL 179, /A LEU 191, /A ASP 241 
    3017 195 hydrogen bonds 
    3018 Adding 'H' to /A TYR 27 
    3019 Adding 'H' to /A PHE 174 
    3020 Adding 'H' to /A THR 181 
    3021 Adding 'H' to /A GLY 194 
    3022 Adding 'H' to /A LEU 248 
    3023 /A GLU 24 is not terminus, removing H atom from 'C' 
    3024 /A ALA 165 is not terminus, removing H atom from 'C' 
    3025 /A VAL 179 is not terminus, removing H atom from 'C' 
    3026 /A LEU 191 is not terminus, removing H atom from 'C' 
    3027 /A ASP 241 is not terminus, removing H atom from 'C' 
    3028 -9 hydrogens added 
    3029  
    3030 
    3031 > wait 5
    3032 
    3033 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--
    3034 > WRM-16.result.pdbqt
    3035 
    3036 Summary of feedback from opening
    3037 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--WRM-16.result.pdbqt 
    3038 --- 
    3039 warnings | Ignored bad PDB record found on line 2 
    3040 REMARK VINA RESULT: -7.2 0.000 0.000 
    3041  
    3042 Ignored bad PDB record found on line 3 
    3043 REMARK 5 active torsions: 
    3044  
    3045 Ignored bad PDB record found on line 4 
    3046 REMARK status: ('A' for Active; 'I' for Inactive) 
    3047  
    3048 Ignored bad PDB record found on line 5 
    3049 REMARK 1 A between atoms: C_9 and O_15 
    3050  
    3051 Ignored bad PDB record found on line 6 
    3052 REMARK 2 A between atoms: C_10 and O_17 
    3053  
    3054 184 messages similar to the above omitted 
    3055  
    3056 Opened 5AX3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    3057 bonds) 
    3058 
    3059 > wait 5
    3060 
    3061 > close #2.2-9
    3062 
    3063 > wait 5
    3064 
    3065 > contacts :UNL radius 0.05 log true saveFile
    3066 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
    3067 > WRM-16.contacts.txt
    3068    
    3069    
    3070     Allowed overlap: -0.4
    3071     H-bond overlap reduction: 0.4
    3072     Ignore contacts between atoms separated by 4 bonds or less
    3073     Detect intra-residue contacts: False
    3074     Detect intra-molecule contacts: True
    3075    
    3076     52 contacts
    3077                      atom1                               atom2             overlap  distance
    3078     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLN 345 HG1   0.154    2.606
    3079     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG2   0.099    2.661
    3080     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A PRO 14 HD1    0.056    2.404
    3081     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ILE 81 CG2    0.037    3.543
    3082     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ILE 81 3HG2   0.002    2.878
    3083     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A PRO 14 HD1    -0.003    2.423
    3084     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 84 HG2    -0.004    2.764
    3085     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A GLY 13 HA1    -0.068    2.488
    3086     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG2   -0.084    2.844
    3087     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HB2   -0.109    2.719
    3088     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLY 13 HA1    -0.127    3.007
    3089     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A PRO 14 CD     -0.127    3.247
    3090     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ARG 15 HE     -0.129    2.889
    3091     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ARG 82 O      -0.141    3.501
    3092     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HD2   -0.141    2.901
    3093     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ILE 81 2HG2   -0.151    3.031
    3094     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLN 345 HG1   -0.154    2.914
    3095     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG2   -0.158    2.768
    3096     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG1   -0.158    2.768
    3097     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A ARG 15 CB     -0.174    3.294
    3098     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 84 CG     -0.181    3.641
    3099     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HB2   -0.184    2.794
    3100     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ASP 79 OD2    -0.194    3.434
    3101     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HB2   -0.210    2.970
    3102     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CB    -0.218    3.528
    3103     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG1   -0.235    2.845
    3104     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLY 13 HA1    -0.241    3.121
    3105     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG1   -0.249    2.859
    3106     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLN 345 CG    -0.250    3.710
    3107     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ARG 82 O      -0.279    3.519
    3108     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A GLY 13 CA     -0.284    3.404
    3109     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLY 347 HN    -0.284    3.044
    3110     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG2   -0.287    3.047
    3111     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A ILE 81 CG2    -0.288    3.448
    3112     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A ARG 15 HB1    -0.297    2.717
    3113     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A PRO 14 CD     -0.304    3.464
    3114     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CG    -0.311    3.771
    3115     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A ARG 15 HE     -0.322    2.932
    3116     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CB    -0.324    3.634
    3117     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A ARG 15 HN     -0.330    2.350
    3118     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CG    -0.346    3.806
    3119     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLY 347 HN    -0.347    3.107
    3120     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CG    -0.353    3.663
    3121     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A GLY 347 N     -0.365    3.750
    3122     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 84 HG2    -0.368    3.128
    3123     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A PRO 346 HB2   -0.371    2.831
    3124     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG1   -0.379    2.989
    3125     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HG1   -0.386    2.996
    3126     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CG    -0.388    3.698
    3127     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 CG    -0.391    3.851
    3128     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 346 HD2   -0.396    3.006
    3129     5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C  5AX3.pdbqt #1/A PRO 84 HA     -0.399    3.159
    3130    
    3131 
    3132  
    3133 52 contacts 
    3134 
    3135 > hbonds :UNL showDist true radius 0.05 log true saveFile
    3136 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
    3137 > WRM-16.hbonds.txt
    3138    
    3139    
    3140     Finding intermodel H-bonds
    3141     Finding intramodel H-bonds
    3142     Constraints relaxed by 0.4 angstroms and 20 degrees
    3143     Models used:
    3144         1 5AX3.pdbqt
    3145         2.1 5AX3--WRM-16.result.pdbqt
    3146    
    3147     1 H-bonds
    3148     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    3149     5AX3.pdbqt #1/A ARG 15 N  5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O  5AX3.pdbqt #1/A ARG 15 HN  3.304  2.350
    3150    
    3151 
    3152  
    3153 1 hydrogen bonds found 
    3154 
    3155 > select :UNL
    3156 
    3157 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3158 
    3159 > label sel text "Ligand "
    3160 
    3161 > label height 1
    3162 
    3163 > ~select
    3164 
    3165 Nothing selected 
    3166 
    3167 > 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
    3168 > ypos .95
    3169 
    3170 > 2dlabels text "5AX3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    3171 
    3172 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
    3173 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    3174 > true
    3175 
    3176 > select :UNL
    3177 
    3178 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3179 
    3180 > view sel
    3181 
    3182 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
    3183 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    3184 > true
    3185 
    3186 > close
    3187 
    3188 > wait 5
    3189 
    3190 > set bgColor white
    3191 
    3192 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KMU.pdbqt
    3193 
    3194 Chain information for 2KMU.pdbqt #1 
    3195 --- 
    3196 Chain | Description 
    3197 A | No description available 
    3198  
    3199 Opened 2KMU.pdbqt containing 1 structures (957 atoms, 963 bonds) 
    3200 
    3201 > wait 5
    3202 
    3203 > hide surfaces
    3204 
    3205 > hide atoms
    3206 
    3207 > show cartoons
    3208 
    3209 > wait 5
    3210 
    3211 > addh
    3212 
    3213 Summary of feedback from adding hydrogens to 2KMU.pdbqt #1 
    3214 --- 
    3215 notes | No usable SEQRES records for 2KMU.pdbqt (#1) chain A; guessing termini
    3216 instead 
    3217 Chain-initial residues that are actual N termini: /A GLY 1 
    3218 Chain-initial residues that are not actual N termini: 
    3219 Chain-final residues that are actual C termini: /A GLN 56 
    3220 Chain-final residues that are not actual C termini: 
    3221 40 hydrogen bonds 
    3222 1 hydrogens added 
    3223  
    3224 
    3225 > wait 5
    3226 
    3227 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--
    3228 > WRM-16.result.pdbqt
    3229 
    3230 Summary of feedback from opening
    3231 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--WRM-16.result.pdbqt 
    3232 --- 
    3233 warnings | Ignored bad PDB record found on line 2 
    3234 REMARK VINA RESULT: -6.8 0.000 0.000 
    3235  
    3236 Ignored bad PDB record found on line 3 
    3237 REMARK 5 active torsions: 
    3238  
    3239 Ignored bad PDB record found on line 4 
    3240 REMARK status: ('A' for Active; 'I' for Inactive) 
    3241  
    3242 Ignored bad PDB record found on line 5 
    3243 REMARK 1 A between atoms: C_9 and O_15 
    3244  
    3245 Ignored bad PDB record found on line 6 
    3246 REMARK 2 A between atoms: C_10 and O_17 
    3247  
    3248 184 messages similar to the above omitted 
    3249  
    3250 Opened 2KMU--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    3251 bonds) 
    3252 
    3253 > wait 5
    3254 
    3255 > close #2.2-9
    3256 
    3257 > wait 5
    3258 
    3259 > contacts :UNL radius 0.05 log true saveFile
    3260 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
    3261 > WRM-16.contacts.txt
    3262    
    3263    
    3264     Allowed overlap: -0.4
    3265     H-bond overlap reduction: 0.4
    3266     Ignore contacts between atoms separated by 4 bonds or less
    3267     Detect intra-residue contacts: False
    3268     Detect intra-molecule contacts: True
    3269    
    3270     55 contacts
    3271                       atom1                               atom2             overlap  distance
    3272     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 HB2    0.691    2.069
    3273     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 CB     0.326    3.134
    3274     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 1HH2   0.311    2.449
    3275     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 NH2    0.233    3.152
    3276     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 HB2    0.185    2.575
    3277     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TYR 44 HE2    0.153    2.727
    3278     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 1HH2   0.129    2.631
    3279     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HE3    0.035    2.575
    3280     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HZ3    0.021    2.589
    3281     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TYR 44 OH     -0.037    3.147
    3282     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KMU.pdbqt #1/A TRP 16 HA     -0.042    2.502
    3283     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 HD3    -0.069    2.829
    3284     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TYR 44 HH     -0.072    2.682
    3285     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TYR 44 CE2    -0.105    3.685
    3286     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 HD3    -0.109    2.869
    3287     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KMU.pdbqt #1/A ARG 12 NH1    -0.111    2.796
    3288     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 CB     -0.121    3.581
    3289     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 NE     -0.127    3.512
    3290     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 36 HB1    -0.128    2.738
    3291     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 12 NH1    -0.135    3.370
    3292     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 HE     -0.136    2.896
    3293     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A THR 40 2HG2   -0.154    2.914
    3294     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CD     -0.168    3.628
    3295     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 NH2    -0.173    3.558
    3296     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HZ3    -0.176    2.786
    3297     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CD     -0.188    3.648
    3298     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HE3    -0.191    2.801
    3299     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 12 NH1    -0.202    3.587
    3300     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 CE3    -0.202    3.512
    3301     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 CB     -0.205    3.785
    3302     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 24 CZ     -0.217    3.677
    3303     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 C      -0.231    3.691
    3304     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 15 O      -0.232    3.592
    3305     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 36 HB1    -0.241    3.121
    3306     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 CZ3    -0.251    3.561
    3307     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 HB1    -0.264    3.144
    3308     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CD     -0.289    3.749
    3309     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HZ3    -0.305    3.065
    3310     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A THR 40 OG1    -0.306    3.566
    3311     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CD     -0.310    3.770
    3312     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KMU.pdbqt #1/A TRP 16 CA     -0.310    3.470
    3313     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 HD2    -0.313    3.073
    3314     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PHE 20 N      -0.315    3.700
    3315     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CG     -0.334    3.794
    3316     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2KMU.pdbqt #1/A PRO 37 HG3    -0.336    3.216
    3317     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KMU.pdbqt #1/A ALA 15 O      -0.344    3.284
    3318     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O   2KMU.pdbqt #1/A ARG 12 2HH1   -0.344    2.404
    3319     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 19 C      -0.359    3.819
    3320     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PHE 20 N      -0.363    3.748
    3321     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A PRO 37 CD     -0.364    3.674
    3322     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 CZ3    -0.366    3.676
    3323     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ALA 36 CB     -0.371    3.681
    3324     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TYR 44 OH     -0.376    3.756
    3325     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A ARG 12 1HH1   -0.384    3.144
    3326     2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C   2KMU.pdbqt #1/A TRP 16 HZ3    -0.391    3.001
    3327    
    3328 
    3329  
    3330 55 contacts 
    3331 
    3332 > hbonds :UNL showDist true radius 0.05 log true saveFile
    3333 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
    3334 > WRM-16.hbonds.txt
    3335    
    3336    
    3337     Finding intermodel H-bonds
    3338     Finding intramodel H-bonds
    3339     Constraints relaxed by 0.4 angstroms and 20 degrees
    3340     Models used:
    3341         1 2KMU.pdbqt
    3342         2.1 2KMU--WRM-16.result.pdbqt
    3343    
    3344     0 H-bonds
    3345     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    3346    
    3347 
    3348  
    3349 0 hydrogen bonds found 
    3350 
    3351 > select :UNL
    3352 
    3353 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3354 
    3355 > label sel text "Ligand "
    3356 
    3357 > label height 1
    3358 
    3359 > ~select
    3360 
    3361 Nothing selected 
    3362 
    3363 > 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
    3364 > ypos .95
    3365 
    3366 > 2dlabels text "2KMU WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    3367 
    3368 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
    3369 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    3370 > true
    3371 
    3372 > select :UNL
    3373 
    3374 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3375 
    3376 > view sel
    3377 
    3378 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
    3379 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    3380 > true
    3381 
    3382 > close
    3383 
    3384 > wait 5
    3385 
    3386 > set bgColor white
    3387 
    3388 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D68.pdbqt
    3389 
    3390 Chain information for 2D68.pdbqt #1 
    3391 --- 
    3392 Chain | Description 
    3393 A | No description available 
    3394 B | No description available 
    3395  
    3396 Opened 2D68.pdbqt containing 1 structures (2419 atoms, 2436 bonds) 
    3397 
    3398 > wait 5
    3399 
    3400 > hide surfaces
    3401 
    3402 > hide atoms
    3403 
    3404 > show cartoons
    3405 
    3406 > wait 5
    3407 
    3408 > addh
    3409 
    3410 Summary of feedback from adding hydrogens to 2D68.pdbqt #1 
    3411 --- 
    3412 warnings | Not adding hydrogens to /A LYS 69 CD because it is missing heavy-
    3413 atom bond partners 
    3414 Not adding hydrogens to /B LYS 69 CG because it is missing heavy-atom bond
    3415 partners 
    3416 notes | No usable SEQRES records for 2D68.pdbqt (#1) chain A; guessing termini
    3417 instead 
    3418 No usable SEQRES records for 2D68.pdbqt (#1) chain B; guessing termini instead 
    3419 Chain-initial residues that are actual N termini: /A VAL 58, /B ASN 59 
    3420 Chain-initial residues that are not actual N termini: /A LEU 104 
    3421 Chain-final residues that are actual C termini: /A TRP 135, /B TRP 135 
    3422 Chain-final residues that are not actual C termini: /A THR 100 
    3423 143 hydrogen bonds 
    3424 Adding 'H' to /A LEU 104 
    3425 /A THR 100 is not terminus, removing H atom from 'C' 
    3426 -3 hydrogens added 
    3427  
    3428 
    3429 > wait 5
    3430 
    3431 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--
    3432 > WRM-16.result.pdbqt
    3433 
    3434 Summary of feedback from opening
    3435 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--WRM-16.result.pdbqt 
    3436 --- 
    3437 warnings | Ignored bad PDB record found on line 2 
    3438 REMARK VINA RESULT: -6.5 0.000 0.000 
    3439  
    3440 Ignored bad PDB record found on line 3 
    3441 REMARK 5 active torsions: 
    3442  
    3443 Ignored bad PDB record found on line 4 
    3444 REMARK status: ('A' for Active; 'I' for Inactive) 
    3445  
    3446 Ignored bad PDB record found on line 5 
    3447 REMARK 1 A between atoms: C_9 and O_15 
    3448  
    3449 Ignored bad PDB record found on line 6 
    3450 REMARK 2 A between atoms: C_10 and O_17 
    3451  
    3452 184 messages similar to the above omitted 
    3453  
    3454 Opened 2D68--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    3455 bonds) 
    3456 
    3457 > wait 5
    3458 
    3459 > close #2.2-9
    3460 
    3461 > wait 5
    3462 
    3463 > contacts :UNL radius 0.05 log true saveFile
    3464 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
    3465 > WRM-16.contacts.txt
    3466    
    3467    
    3468     Allowed overlap: -0.4
    3469     H-bond overlap reduction: 0.4
    3470     Ignore contacts between atoms separated by 4 bonds or less
    3471     Detect intra-residue contacts: False
    3472     Detect intra-molecule contacts: True
    3473    
    3474     45 contacts
    3475                       atom1                              atom2             overlap  distance
    3476     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HD2   0.473    2.407
    3477     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HD1   0.376    2.384
    3478     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 HB1   0.240    2.640
    3479     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 HA    0.211    2.669
    3480     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 CD    0.179    3.281
    3481     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B PHE 65 HD1   0.147    2.733
    3482     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 CD    0.095    3.485
    3483     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HD1   0.057    2.703
    3484     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 HD1   0.023    2.437
    3485     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 HA    0.004    2.456
    3486     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 CB    -0.002    3.582
    3487     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 HD1   -0.029    2.449
    3488     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 CD1   -0.031    3.151
    3489     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/A PHE 85 HZ    -0.041    2.461
    3490     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.069    2.829
    3491     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A PHE 84 CZ    -0.108    3.568
    3492     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A GLY 124 O    -0.108    3.468
    3493     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2D68.pdbqt #1/A PHE 84 O     -0.119    3.479
    3494     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 CA    -0.139    3.719
    3495     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.157    2.917
    3496     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A PHE 84 O     -0.164    3.404
    3497     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 CA    -0.169    3.329
    3498     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/A PHE 85 CZ    -0.174    3.294
    3499     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B PHE 65 CD1   -0.195    3.775
    3500     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/A PHE 84 HE2   -0.224    2.684
    3501     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A PHE 84 CE2   -0.261    3.721
    3502     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 CD1   -0.269    3.429
    3503     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A PHE 84 CZ    -0.272    3.582
    3504     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 CD    -0.275    3.735
    3505     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.282    2.892
    3506     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.283    3.043
    3507     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.310    3.070
    3508     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2D68.pdbqt #1/A PHE 84 CE1   -0.322    3.902
    3509     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/A GLY 124 O    -0.324    3.414
    3510     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HD2   -0.344    3.104
    3511     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B SER 61 HB1   -0.355    2.815
    3512     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/A GLY 124 O    -0.356    3.296
    3513     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 CB    -0.368    3.828
    3514     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2D68.pdbqt #1/A PHE 84 CD1   -0.372    3.952
    3515     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 CB    -0.384    3.844
    3516     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 HB1   -0.385    2.995
    3517     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 CA    -0.390    3.970
    3518     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B SER 61 HB1   -0.391    3.151
    3519     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D68.pdbqt #1/B LYS 64 CB    -0.395    3.705
    3520     2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D68.pdbqt #1/B PHE 65 CB    -0.395    3.555
    3521    
    3522 
    3523  
    3524 45 contacts 
    3525 
    3526 > hbonds :UNL showDist true radius 0.05 log true saveFile
    3527 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
    3528 > WRM-16.hbonds.txt
    3529    
    3530    
    3531     Finding intermodel H-bonds
    3532     Finding intramodel H-bonds
    3533     Constraints relaxed by 0.4 angstroms and 20 degrees
    3534     Models used:
    3535         1 2D68.pdbqt
    3536         2.1 2D68--WRM-16.result.pdbqt
    3537    
    3538     0 H-bonds
    3539     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    3540    
    3541 
    3542  
    3543 0 hydrogen bonds found 
    3544 
    3545 > select :UNL
    3546 
    3547 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3548 
    3549 > label sel text "Ligand "
    3550 
    3551 > label height 1
    3552 
    3553 > ~select
    3554 
    3555 Nothing selected 
    3556 
    3557 > 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
    3558 > ypos .95
    3559 
    3560 > 2dlabels text "2D68 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    3561 
    3562 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
    3563 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    3564 > true
    3565 
    3566 > select :UNL
    3567 
    3568 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3569 
    3570 > view sel
    3571 
    3572 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
    3573 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    3574 > true
    3575 
    3576 > close
    3577 
    3578 > wait 5
    3579 
    3580 > set bgColor white
    3581 
    3582 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OW1.pdbqt
    3583 
    3584 Chain information for 1OW1.pdbqt #1 
    3585 --- 
    3586 Chain | Description 
    3587 A | No description available 
    3588  
    3589 Opened 1OW1.pdbqt containing 1 structures (2619 atoms, 2644 bonds) 
    3590 
    3591 > wait 5
    3592 
    3593 > hide surfaces
    3594 
    3595 > hide atoms
    3596 
    3597 > show cartoons
    3598 
    3599 > wait 5
    3600 
    3601 > addh
    3602 
    3603 Summary of feedback from adding hydrogens to 1OW1.pdbqt #1 
    3604 --- 
    3605 notes | No usable SEQRES records for 1OW1.pdbqt (#1) chain A; guessing termini
    3606 instead 
    3607 Chain-initial residues that are actual N termini: /A PRO 3495 
    3608 Chain-initial residues that are not actual N termini: /A PRO 3545 
    3609 Chain-final residues that are actual C termini: /A VAL 3664 
    3610 Chain-final residues that are not actual C termini: /A SER 3541 
    3611 124 hydrogen bonds 
    3612 /A SER 3541 is not terminus, removing H atom from 'C' 
    3613 0 hydrogens added 
    3614  
    3615 
    3616 > wait 5
    3617 
    3618 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--
    3619 > WRM-16.result.pdbqt
    3620 
    3621 Summary of feedback from opening
    3622 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--WRM-16.result.pdbqt 
    3623 --- 
    3624 warnings | Ignored bad PDB record found on line 2 
    3625 REMARK VINA RESULT: -7.1 0.000 0.000 
    3626  
    3627 Ignored bad PDB record found on line 3 
    3628 REMARK 5 active torsions: 
    3629  
    3630 Ignored bad PDB record found on line 4 
    3631 REMARK status: ('A' for Active; 'I' for Inactive) 
    3632  
    3633 Ignored bad PDB record found on line 5 
    3634 REMARK 1 A between atoms: C_9 and O_15 
    3635  
    3636 Ignored bad PDB record found on line 6 
    3637 REMARK 2 A between atoms: C_10 and O_17 
    3638  
    3639 184 messages similar to the above omitted 
    3640  
    3641 Opened 1OW1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    3642 bonds) 
    3643 
    3644 > wait 5
    3645 
    3646 > close #2.2-9
    3647 
    3648 > wait 5
    3649 
    3650 > contacts :UNL radius 0.05 log true saveFile
    3651 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
    3652 > WRM-16.contacts.txt
    3653    
    3654    
    3655     Allowed overlap: -0.4
    3656     H-bond overlap reduction: 0.4
    3657     Ignore contacts between atoms separated by 4 bonds or less
    3658     Detect intra-residue contacts: False
    3659     Detect intra-molecule contacts: True
    3660    
    3661     54 contacts
    3662                       atom1                                atom2              overlap  distance
    3663     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB2    0.457    2.423
    3664     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A HIS 3656 HE1    0.285    2.595
    3665     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 1HG2   0.241    2.639
    3666     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A LYS 3596 HD2    0.208    2.552
    3667     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A HIS 3656 CE1    0.058    3.522
    3668     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ASN 3652 ND2    0.047    3.188
    3669     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 CB     0.042    3.538
    3670     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ASN 3652 1HD2   0.027    2.583
    3671     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLN 3604 1HE2   0.008    2.602
    3672     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A GLN 3604 1HE2   0.006    2.054
    3673     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLU 3636 OE2    -0.046    3.286
    3674     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 CG2    -0.051    3.511
    3675     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HG2    -0.056    2.936
    3676     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A LYS 3596 CD     -0.060    3.520
    3677     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB2    -0.069    2.679
    3678     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A PRO 3655 HG1    -0.070    2.490
    3679     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 2HD1   -0.102    2.982
    3680     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 ND2    -0.113    2.798
    3681     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A LYS 3596 HG1    -0.117    2.537
    3682     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 CG2    -0.123    3.703
    3683     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1OW1.pdbqt #1/A THR 3601 OG1    -0.128    3.508
    3684     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 1HD2   -0.143    2.203
    3685     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLN 3604 OE1    -0.160    3.400
    3686     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 CB     -0.161    3.471
    3687     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLU 3636 CD     -0.162    3.622
    3688     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB1    -0.171    2.781
    3689     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 1HG2   -0.189    2.799
    3690     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A PRO 3655 CG     -0.210    3.330
    3691     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 1HG2   -0.214    2.974
    3692     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A SER 3651 HA     -0.252    3.132
    3693     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB1    -0.262    2.872
    3694     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 HN     -0.264    2.284
    3695     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 CB     -0.265    3.575
    3696     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 CB     -0.274    3.584
    3697     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A LYS 3596 CG     -0.287    3.407
    3698     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLN 3604 OE1    -0.287    3.527
    3699     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A PRO 3655 CB     -0.295    3.415
    3700     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 HN     -0.297    2.357
    3701     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 CG     -0.300    3.880
    3702     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB1    -0.312    2.922
    3703     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLU 3636 CD     -0.313    3.773
    3704     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A LYS 3596 CG     -0.322    3.782
    3705     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A LYS 3596 HB1    -0.332    3.092
    3706     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 N      -0.332    2.977
    3707     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLN 3604 NE2    -0.343    3.578
    3708     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ILE 3600 3HG2   -0.343    3.103
    3709     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A ASN 3652 CA     -0.344    3.464
    3710     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ASN 3652 HN     -0.347    3.227
    3711     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A GLN 3604 NE2    -0.358    3.043
    3712     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O   1OW1.pdbqt #1/A LYS 3596 CD     -0.367    3.487
    3713     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A GLN 3604 NE2    -0.367    3.752
    3714     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ASN 3652 1HD2   -0.377    2.987
    3715     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A PRO 3631 HB2    -0.377    2.987
    3716     1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C   1OW1.pdbqt #1/A ASN 3652 HN     -0.390    3.000
    3717    
    3718 
    3719  
    3720 54 contacts 
    3721 
    3722 > hbonds :UNL showDist true radius 0.05 log true saveFile
    3723 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
    3724 > WRM-16.hbonds.txt
    3725    
    3726    
    3727     Finding intermodel H-bonds
    3728     Finding intramodel H-bonds
    3729     Constraints relaxed by 0.4 angstroms and 20 degrees
    3730     Models used:
    3731         1 1OW1.pdbqt
    3732         2.1 1OW1--WRM-16.result.pdbqt
    3733    
    3734     2 H-bonds
    3735     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    3736     1OW1.pdbqt #1/A GLN 3604 NE2  1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O  1OW1.pdbqt #1/A GLN 3604 1HE2  3.043  2.054
    3737     1OW1.pdbqt #1/A ASN 3652 N    1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O  1OW1.pdbqt #1/A ASN 3652 HN    3.284  2.357
    3738    
    3739 
    3740  
    3741 2 hydrogen bonds found 
    3742 
    3743 > select :UNL
    3744 
    3745 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3746 
    3747 > label sel text "Ligand "
    3748 
    3749 > label height 1
    3750 
    3751 > ~select
    3752 
    3753 Nothing selected 
    3754 
    3755 > 2dlabels text "Binding Energy: -7.1 kcal/mol" color red size 18 xpos .03
    3756 > ypos .95
    3757 
    3758 > 2dlabels text "1OW1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    3759 
    3760 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
    3761 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    3762 > true
    3763 
    3764 > select :UNL
    3765 
    3766 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3767 
    3768 > view sel
    3769 
    3770 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
    3771 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    3772 > true
    3773 
    3774 > close
    3775 
    3776 > wait 5
    3777 
    3778 > set bgColor white
    3779 
    3780 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RJB.pdbqt
    3781 
    3782 Chain information for 1RJB.pdbqt #1 
    3783 --- 
    3784 Chain | Description 
    3785 A | No description available 
    3786  
    3787 Opened 1RJB.pdbqt containing 1 structures (4781 atoms, 4839 bonds) 
    3788 
    3789 > wait 5
    3790 
    3791 > hide surfaces
    3792 
    3793 > hide atoms
    3794 
    3795 > show cartoons
    3796 
    3797 > wait 5
    3798 
    3799 > addh
    3800 
    3801 Summary of feedback from adding hydrogens to 1RJB.pdbqt #1 
    3802 --- 
    3803 notes | No usable SEQRES records for 1RJB.pdbqt (#1) chain A; guessing termini
    3804 instead 
    3805 Chain-initial residues that are actual N termini: /A TYR 572 
    3806 Chain-initial residues that are not actual N termini: /A ARG 655, /A LEU 783 
    3807 Chain-final residues that are actual C termini: /A LEU 947 
    3808 Chain-final residues that are not actual C termini: /A GLU 648, /A PHE 710 
    3809 249 hydrogen bonds 
    3810 Adding 'H' to /A ARG 655 
    3811 Adding 'H' to /A LEU 783 
    3812 /A GLU 648 is not terminus, removing H atom from 'C' 
    3813 /A PHE 710 is not terminus, removing H atom from 'C' 
    3814 3 hydrogens added 
    3815  
    3816 
    3817 > wait 5
    3818 
    3819 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--
    3820 > WRM-16.result.pdbqt
    3821 
    3822 Summary of feedback from opening
    3823 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--WRM-16.result.pdbqt 
    3824 --- 
    3825 warnings | Ignored bad PDB record found on line 2 
    3826 REMARK VINA RESULT: -8.6 0.000 0.000 
    3827  
    3828 Ignored bad PDB record found on line 3 
    3829 REMARK 5 active torsions: 
    3830  
    3831 Ignored bad PDB record found on line 4 
    3832 REMARK status: ('A' for Active; 'I' for Inactive) 
    3833  
    3834 Ignored bad PDB record found on line 5 
    3835 REMARK 1 A between atoms: C_9 and O_15 
    3836  
    3837 Ignored bad PDB record found on line 6 
    3838 REMARK 2 A between atoms: C_10 and O_17 
    3839  
    3840 184 messages similar to the above omitted 
    3841  
    3842 Opened 1RJB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    3843 bonds) 
    3844 
    3845 > wait 5
    3846 
    3847 > close #2.2-9
    3848 
    3849 > wait 5
    3850 
    3851 > contacts :UNL radius 0.05 log true saveFile
    3852 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
    3853 > WRM-16.contacts.txt
    3854    
    3855    
    3856     Allowed overlap: -0.4
    3857     H-bond overlap reduction: 0.4
    3858     Ignore contacts between atoms separated by 4 bonds or less
    3859     Detect intra-residue contacts: False
    3860     Detect intra-molecule contacts: True
    3861    
    3862     51 contacts
    3863                      atom1                               atom2              overlap  distance
    3864     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 2HE2   0.378    2.502
    3865     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ILE 836 2HG2   0.292    2.468
    3866     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 NE2    0.238    3.267
    3867     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A PHE 621 HE2    0.094    2.666
    3868     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A TYR 865 HH     0.037    2.723
    3869     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 O      0.021    3.069
    3870     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ILE 836 1HG1   -0.003    2.763
    3871     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 CG     -0.016    3.596
    3872     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ALA 848 HB3    -0.091    2.851
    3873     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HB1    -0.091    2.701
    3874     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 CD     -0.093    3.403
    3875     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ILE 836 CG2    -0.117    3.577
    3876     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HG1    -0.148    2.908
    3877     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ARG 810 HD2    -0.162    2.582
    3878     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HN     -0.174    2.784
    3879     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HG1    -0.178    2.938
    3880     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A LEU 850 1HD2   -0.179    2.939
    3881     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A TYR 842 CE1    -0.179    3.339
    3882     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A LEU 850 1HD2   -0.188    2.948
    3883     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A PHE 621 CE2    -0.192    3.652
    3884     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ILE 836 2HG2   -0.200    2.960
    3885     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ALA 848 HA     -0.214    2.674
    3886     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ARG 810 CD     -0.219    3.339
    3887     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 HG2    -0.221    3.101
    3888     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 CG     -0.223    3.683
    3889     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ASP 811 HB2    -0.228    2.648
    3890     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A GLN 575 HG2    -0.230    2.650
    3891     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 CG     -0.243    3.703
    3892     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A LEU 850 CD2    -0.254    3.714
    3893     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 HG1    -0.259    3.139
    3894     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 CD     -0.259    3.839
    3895     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A TYR 865 OH     -0.259    3.519
    3896     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 OE1    -0.268    3.358
    3897     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 O      -0.269    3.359
    3898     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ALA 848 CB     -0.277    3.737
    3899     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 O      -0.297    3.387
    3900     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 O      -0.301    3.391
    3901     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HG2    -0.313    3.073
    3902     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 NE2    -0.318    3.553
    3903     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HB1    -0.331    3.091
    3904     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 OE1    -0.332    3.692
    3905     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 NE2    -0.352    3.857
    3906     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 CD     -0.357    3.667
    3907     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 OE1    -0.366    3.726
    3908     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A TYR 842 HE1    -0.375    2.835
    3909     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ARG 810 CZ     -0.376    3.496
    3910     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ASP 811 OD1    -0.387    3.747
    3911     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A GLN 575 CD     -0.389    3.969
    3912     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ARG 849 HB1    -0.395    3.005
    3913     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C  1RJB.pdbqt #1/A ILE 836 CG1    -0.395    3.855
    3914     1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O  1RJB.pdbqt #1/A ASP 811 CB     -0.397    3.517
    3915    
    3916 
    3917  
    3918 51 contacts 
    3919 
    3920 > hbonds :UNL showDist true radius 0.05 log true saveFile
    3921 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
    3922 > WRM-16.hbonds.txt
    3923    
    3924    
    3925     Finding intermodel H-bonds
    3926     Finding intramodel H-bonds
    3927     Constraints relaxed by 0.4 angstroms and 20 degrees
    3928     Models used:
    3929         1 1RJB.pdbqt
    3930         2.1 1RJB--WRM-16.result.pdbqt
    3931    
    3932     0 H-bonds
    3933     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    3934    
    3935 
    3936  
    3937 0 hydrogen bonds found 
    3938 
    3939 > select :UNL
    3940 
    3941 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3942 
    3943 > label sel text "Ligand "
    3944 
    3945 > label height 1
    3946 
    3947 > ~select
    3948 
    3949 Nothing selected 
    3950 
    3951 > 2dlabels text "Binding Energy: -8.6 kcal/mol" color red size 18 xpos .03
    3952 > ypos .95
    3953 
    3954 > 2dlabels text "1RJB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    3955 
    3956 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
    3957 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    3958 > true
    3959 
    3960 > select :UNL
    3961 
    3962 28 atoms, 31 bonds, 1 residue, 1 model selected 
    3963 
    3964 > view sel
    3965 
    3966 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
    3967 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    3968 > true
    3969 
    3970 > close
    3971 
    3972 > wait 5
    3973 
    3974 > set bgColor white
    3975 
    3976 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1IFR.pdbqt
    3977 
    3978 Chain information for 1IFR.pdbqt #1 
    3979 --- 
    3980 Chain | Description 
    3981 A | No description available 
    3982  
    3983 Opened 1IFR.pdbqt containing 1 structures (1747 atoms, 1765 bonds) 
    3984 
    3985 > wait 5
    3986 
    3987 > hide surfaces
    3988 
    3989 > hide atoms
    3990 
    3991 > show cartoons
    3992 
    3993 > wait 5
    3994 
    3995 > addh
    3996 
    3997 Summary of feedback from adding hydrogens to 1IFR.pdbqt #1 
    3998 --- 
    3999 notes | No usable SEQRES records for 1IFR.pdbqt (#1) chain A; guessing termini
    4000 instead 
    4001 Chain-initial residues that are actual N termini: /A GLY 432 
    4002 Chain-initial residues that are not actual N termini: 
    4003 Chain-final residues that are actual C termini: /A VAL 544 
    4004 Chain-final residues that are not actual C termini: 
    4005 96 hydrogen bonds 
    4006 1 hydrogens added 
    4007  
    4008 
    4009 > wait 5
    4010 
    4011 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--
    4012 > WRM-16.result.pdbqt
    4013 
    4014 Summary of feedback from opening
    4015 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--WRM-16.result.pdbqt 
    4016 --- 
    4017 warnings | Ignored bad PDB record found on line 2 
    4018 REMARK VINA RESULT: -6.7 0.000 0.000 
    4019  
    4020 Ignored bad PDB record found on line 3 
    4021 REMARK 5 active torsions: 
    4022  
    4023 Ignored bad PDB record found on line 4 
    4024 REMARK status: ('A' for Active; 'I' for Inactive) 
    4025  
    4026 Ignored bad PDB record found on line 5 
    4027 REMARK 1 A between atoms: C_9 and O_15 
    4028  
    4029 Ignored bad PDB record found on line 6 
    4030 REMARK 2 A between atoms: C_10 and O_17 
    4031  
    4032 184 messages similar to the above omitted 
    4033  
    4034 Opened 1IFR--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4035 bonds) 
    4036 
    4037 > wait 5
    4038 
    4039 > close #2.2-9
    4040 
    4041 > wait 5
    4042 
    4043 > contacts :UNL radius 0.05 log true saveFile
    4044 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
    4045 > WRM-16.contacts.txt
    4046    
    4047    
    4048     Allowed overlap: -0.4
    4049     H-bond overlap reduction: 0.4
    4050     Ignore contacts between atoms separated by 4 bonds or less
    4051     Detect intra-residue contacts: False
    4052     Detect intra-molecule contacts: True
    4053    
    4054     43 contacts
    4055                      atom1                               atom2             overlap  distance
    4056     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TYR 481 HE1   0.513    2.367
    4057     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TYR 481 CE1   0.243    3.337
    4058     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A PRO 484 HA    0.157    2.723
    4059     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HD2   0.117    2.643
    4060     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TRP 514 HE1   0.011    2.869
    4061     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 CE1   -0.034    3.494
    4062     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A TRP 514 HD1   -0.075    2.495
    4063     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ALA 516 HB1   -0.130    3.010
    4064     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ALA 516 CB    -0.132    3.712
    4065     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 CE1   -0.132    3.442
    4066     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 CB    -0.156    3.616
    4067     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A PRO 484 CA    -0.164    3.744
    4068     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 CD    -0.170    3.630
    4069     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A VAL 513 O     -0.173    3.533
    4070     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HB1   -0.177    2.937
    4071     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A LYS 515 HN    -0.199    2.809
    4072     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A PRO 484 HG1   -0.203    2.963
    4073     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HB1   -0.212    2.972
    4074     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A VAL 513 O     -0.218    3.458
    4075     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TRP 514 NE1   -0.230    3.735
    4076     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 CE1   -0.238    3.698
    4077     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A LYS 515 HB2   -0.256    2.676
    4078     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A LEU 512 HB1   -0.279    2.699
    4079     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HB1   -0.284    3.044
    4080     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TYR 481 OH    -0.290    3.670
    4081     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TRP 514 HD1   -0.300    2.910
    4082     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A PRO 484 HG1   -0.303    2.723
    4083     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 CB    -0.312    3.772
    4084     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 NE2   -0.315    3.700
    4085     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A PRO 484 HA    -0.316    2.776
    4086     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 CE1   -0.321    3.781
    4087     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A ALA 516 HN    -0.348    2.368
    4088     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 CB    -0.362    3.822
    4089     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HD2   -0.363    3.123
    4090     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HB1   -0.365    3.125
    4091     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 ND1   -0.367    3.752
    4092     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A TYR 481 CZ    -0.368    3.948
    4093     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 HB2   -0.368    3.128
    4094     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 CD    -0.382    3.842
    4095     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A HIS 506 HE1   -0.384    2.994
    4096     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A HIS 506 HE1   -0.385    2.805
    4097     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A TRP 514 CD1   -0.396    3.516
    4098     1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C  1IFR.pdbqt #1/A ARG 482 O     -0.398    3.488
    4099    
    4100 
    4101  
    4102 43 contacts 
    4103 
    4104 > hbonds :UNL showDist true radius 0.05 log true saveFile
    4105 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
    4106 > WRM-16.hbonds.txt
    4107    
    4108    
    4109     Finding intermodel H-bonds
    4110     Finding intramodel H-bonds
    4111     Constraints relaxed by 0.4 angstroms and 20 degrees
    4112     Models used:
    4113         1 1IFR.pdbqt
    4114         2.1 1IFR--WRM-16.result.pdbqt
    4115    
    4116     2 H-bonds
    4117     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    4118     1IFR.pdbqt #1/A LYS 515 N  1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A LYS 515 HN  3.558  2.542
    4119     1IFR.pdbqt #1/A ALA 516 N  1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O  1IFR.pdbqt #1/A ALA 516 HN  3.125  2.368
    4120    
    4121 
    4122  
    4123 2 hydrogen bonds found 
    4124 
    4125 > select :UNL
    4126 
    4127 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4128 
    4129 > label sel text "Ligand "
    4130 
    4131 > label height 1
    4132 
    4133 > ~select
    4134 
    4135 Nothing selected 
    4136 
    4137 > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
    4138 > ypos .95
    4139 
    4140 > 2dlabels text "1IFR WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    4141 
    4142 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
    4143 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    4144 > true
    4145 
    4146 > select :UNL
    4147 
    4148 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4149 
    4150 > view sel
    4151 
    4152 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
    4153 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    4154 > true
    4155 
    4156 > close
    4157 
    4158 > wait 5
    4159 
    4160 > set bgColor white
    4161 
    4162 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1DNQ.pdbqt
    4163 
    4164 Chain information for 1DNQ.pdbqt #1 
    4165 --- 
    4166 Chain | Description 
    4167 A | No description available 
    4168  
    4169 Opened 1DNQ.pdbqt containing 1 structures (4770 atoms, 4812 bonds) 
    4170 
    4171 > wait 5
    4172 
    4173 > hide surfaces
    4174 
    4175 > hide atoms
    4176 
    4177 > show cartoons
    4178 
    4179 > wait 5
    4180 
    4181 > addh
    4182 
    4183 Summary of feedback from adding hydrogens to 1DNQ.pdbqt #1 
    4184 --- 
    4185 notes | No usable SEQRES records for 1DNQ.pdbqt (#1) chain A; guessing termini
    4186 instead 
    4187 Chain-initial residues that are actual N termini: /A LEU 1 
    4188 Chain-initial residues that are not actual N termini: 
    4189 Chain-final residues that are actual C termini: /A VAL 312 
    4190 Chain-final residues that are not actual C termini: 
    4191 155 hydrogen bonds 
    4192 26 hydrogens added 
    4193  
    4194 
    4195 > wait 5
    4196 
    4197 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--
    4198 > WRM-16.result.pdbqt
    4199 
    4200 Summary of feedback from opening
    4201 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--WRM-16.result.pdbqt 
    4202 --- 
    4203 warnings | Ignored bad PDB record found on line 2 
    4204 REMARK VINA RESULT: -7.9 0.000 0.000 
    4205  
    4206 Ignored bad PDB record found on line 3 
    4207 REMARK 5 active torsions: 
    4208  
    4209 Ignored bad PDB record found on line 4 
    4210 REMARK status: ('A' for Active; 'I' for Inactive) 
    4211  
    4212 Ignored bad PDB record found on line 5 
    4213 REMARK 1 A between atoms: C_9 and O_15 
    4214  
    4215 Ignored bad PDB record found on line 6 
    4216 REMARK 2 A between atoms: C_10 and O_17 
    4217  
    4218 184 messages similar to the above omitted 
    4219  
    4220 Opened 1DNQ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4221 bonds) 
    4222 
    4223 > wait 5
    4224 
    4225 > close #2.2-9
    4226 
    4227 > wait 5
    4228 
    4229 > contacts :UNL radius 0.05 log true saveFile
    4230 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
    4231 > WRM-16.contacts.txt
    4232    
    4233    
    4234     Allowed overlap: -0.4
    4235     H-bond overlap reduction: 0.4
    4236     Ignore contacts between atoms separated by 4 bonds or less
    4237     Detect intra-residue contacts: False
    4238     Detect intra-molecule contacts: True
    4239    
    4240     44 contacts
    4241                       atom1                               atom2             overlap  distance
    4242     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A TYR 45 HN     0.298    2.582
    4243     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 CD1   0.113    3.467
    4244     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    0.112    2.648
    4245     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1DNQ.pdbqt #1/A ASN 70 1HD2   0.109    1.911
    4246     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 HG2   0.095    2.665
    4247     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ALA 68 HB2    0.074    2.686
    4248     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A TYR 45 N      0.071    3.434
    4249     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    -0.020    2.780
    4250     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A TYR 45 HB1    -0.041    2.921
    4251     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HA     -0.076    2.836
    4252     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    -0.088    2.698
    4253     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    -0.089    2.849
    4254     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 HD1   -0.098    2.978
    4255     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 HA    -0.117    2.877
    4256     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1DNQ.pdbqt #1/A TYR 45 HE1    -0.135    2.555
    4257     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 CE2   -0.142    3.452
    4258     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ALA 68 CB     -0.172    3.632
    4259     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 CG    -0.199    3.659
    4260     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    -0.208    2.968
    4261     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ASN 70 1HD2   -0.212    2.822
    4262     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A TYR 45 CB     -0.218    3.798
    4263     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ASN 104 C     -0.227    3.687
    4264     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 CA    -0.229    3.689
    4265     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CA     -0.237    3.697
    4266     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 N     -0.252    3.637
    4267     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CD1    -0.253    3.713
    4268     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A ALA 68 HB3    -0.257    3.137
    4269     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CD1    -0.260    3.720
    4270     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A ALA 68 CB     -0.260    3.840
    4271     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O   1DNQ.pdbqt #1/A ASN 70 ND2    -0.271    2.916
    4272     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ASN 70 OD1    -0.279    3.519
    4273     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1DNQ.pdbqt #1/A TYR 45 CA     -0.290    3.870
    4274     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A LYS 105 HA    -0.291    3.051
    4275     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 CD2   -0.304    3.614
    4276     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HD1    -0.326    2.936
    4277     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 CZ    -0.334    3.644
    4278     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CD1    -0.353    3.663
    4279     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 HB1    -0.356    2.966
    4280     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ASN 70 OD1    -0.365    3.455
    4281     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 101 CE2   -0.368    3.678
    4282     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CD1    -0.383    3.843
    4283     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A TYR 45 CD1    -0.385    3.845
    4284     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ALA 68 C      -0.385    3.845
    4285     1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C   1DNQ.pdbqt #1/A ALA 103 O     -0.388    3.628
    4286    
    4287 
    4288  
    4289 44 contacts 
    4290 
    4291 > hbonds :UNL showDist true radius 0.05 log true saveFile
    4292 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
    4293 > WRM-16.hbonds.txt
    4294    
    4295    
    4296     Finding intermodel H-bonds
    4297     Finding intramodel H-bonds
    4298     Constraints relaxed by 0.4 angstroms and 20 degrees
    4299     Models used:
    4300         1 1DNQ.pdbqt
    4301         2.1 1DNQ--WRM-16.result.pdbqt
    4302    
    4303     1 H-bonds
    4304     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    4305     1DNQ.pdbqt #1/A ASN 70 ND2  1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O  1DNQ.pdbqt #1/A ASN 70 1HD2  2.916  1.911
    4306    
    4307 
    4308  
    4309 1 hydrogen bonds found 
    4310 
    4311 > select :UNL
    4312 
    4313 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4314 
    4315 > label sel text "Ligand "
    4316 
    4317 > label height 1
    4318 
    4319 > ~select
    4320 
    4321 Nothing selected 
    4322 
    4323 > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
    4324 > ypos .95
    4325 
    4326 > 2dlabels text "1DNQ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    4327 
    4328 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
    4329 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    4330 > true
    4331 
    4332 > select :UNL
    4333 
    4334 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4335 
    4336 > view sel
    4337 
    4338 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
    4339 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    4340 > true
    4341 
    4342 > close
    4343 
    4344 > wait 5
    4345 
    4346 > set bgColor white
    4347 
    4348 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3U84.pdbqt
    4349 
    4350 Chain information for 3U84.pdbqt #1 
    4351 --- 
    4352 Chain | Description 
    4353 A | No description available 
    4354 B | No description available 
    4355  
    4356 Opened 3U84.pdbqt containing 1 structures (15424 atoms, 15596 bonds) 
    4357 
    4358 > wait 5
    4359 
    4360 > hide surfaces
    4361 
    4362 > hide atoms
    4363 
    4364 > show cartoons
    4365 
    4366 > wait 5
    4367 
    4368 > addh
    4369 
    4370 Summary of feedback from adding hydrogens to 3U84.pdbqt #1 
    4371 --- 
    4372 warnings | Not adding hydrogens to /B ARG 206 CB because it is missing heavy-
    4373 atom bond partners 
    4374 Not adding hydrogens to /B ARG 207 CB because it is missing heavy-atom bond
    4375 partners 
    4376 notes | No usable SEQRES records for 3U84.pdbqt (#1) chain A; guessing termini
    4377 instead 
    4378 No usable SEQRES records for 3U84.pdbqt (#1) chain B; guessing termini instead 
    4379 Chain-initial residues that are actual N termini: /A SER 1, /B GLY 2 
    4380 Chain-initial residues that are not actual N termini: /A SER 402, /A THR 534,
    4381 /A GLY 548, /A SER 596, /B LEU 75, /B ARG 206, /B SER 402, /B ALA 523, /B GLY
    4382 548 
    4383 Chain-final residues that are actual C termini: /A LYS 608, /B ALA 581 
    4384 Chain-final residues that are not actual C termini: /A GLY 386, /A GLY 528, /A
    4385 ALA 539, /A ALA 581, /B ASP 70, /B HIS 199, /B ALA 385, /B SER 459, /B GLY 528 
    4386 784 hydrogen bonds 
    4387 Adding 'H' to /A SER 402 
    4388 Adding 'H' to /A THR 534 
    4389 Adding 'H' to /A GLY 548 
    4390 Adding 'H' to /A SER 596 
    4391 Adding 'H' to /B LEU 75 
    4392 4 messages similar to the above omitted 
    4393 /A GLY 386 is not terminus, removing H atom from 'C' 
    4394 /A GLY 528 is not terminus, removing H atom from 'C' 
    4395 /A ALA 539 is not terminus, removing H atom from 'C' 
    4396 /A ALA 581 is not terminus, removing H atom from 'C' 
    4397 /B ASP 70 is not terminus, removing H atom from 'C' 
    4398 4 messages similar to the above omitted 
    4399 -13 hydrogens added 
    4400  
    4401 
    4402 > wait 5
    4403 
    4404 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--
    4405 > WRM-16.result.pdbqt
    4406 
    4407 Summary of feedback from opening
    4408 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--WRM-16.result.pdbqt 
    4409 --- 
    4410 warnings | Ignored bad PDB record found on line 2 
    4411 REMARK VINA RESULT: -7.5 0.000 0.000 
    4412  
    4413 Ignored bad PDB record found on line 3 
    4414 REMARK 5 active torsions: 
    4415  
    4416 Ignored bad PDB record found on line 4 
    4417 REMARK status: ('A' for Active; 'I' for Inactive) 
    4418  
    4419 Ignored bad PDB record found on line 5 
    4420 REMARK 1 A between atoms: C_9 and O_15 
    4421  
    4422 Ignored bad PDB record found on line 6 
    4423 REMARK 2 A between atoms: C_10 and O_17 
    4424  
    4425 184 messages similar to the above omitted 
    4426  
    4427 Opened 3U84--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4428 bonds) 
    4429 
    4430 > wait 5
    4431 
    4432 > close #2.2-9
    4433 
    4434 > wait 5
    4435 
    4436 > contacts :UNL radius 0.05 log true saveFile
    4437 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
    4438 > WRM-16.contacts.txt
    4439    
    4440    
    4441     Allowed overlap: -0.4
    4442     H-bond overlap reduction: 0.4
    4443     Ignore contacts between atoms separated by 4 bonds or less
    4444     Detect intra-residue contacts: False
    4445     Detect intra-molecule contacts: True
    4446    
    4447     37 contacts
    4448                      atom1                               atom2              overlap  distance
    4449     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 HB2    0.433    2.027
    4450     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TRP 341 HZ2    0.260    2.620
    4451     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B VAL 371 1HG1   0.250    2.630
    4452     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B GLY 326 HA1    0.185    2.695
    4453     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B CYS 329 HG     0.091    2.789
    4454     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 CB     0.060    3.100
    4455     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B GLU 363 OE2    -0.030    3.390
    4456     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 319 CD2    -0.086    3.546
    4457     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B VAL 371 CG1    -0.103    3.683
    4458     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B TRP 341 HE1    -0.116    2.136
    4459     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TRP 341 CZ2    -0.126    3.706
    4460     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 HB1    -0.165    2.585
    4461     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B GLY 326 CA     -0.175    3.755
    4462     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B MET 322 HB2    -0.189    3.069
    4463     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 O      -0.208    3.148
    4464     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 CE1    -0.214    3.674
    4465     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B VAL 371 1HG2   -0.215    2.675
    4466     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 CE2    -0.234    3.694
    4467     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B CYS 329 SG     -0.241    3.903
    4468     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 CB     -0.245    3.365
    4469     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 HA     -0.261    3.141
    4470     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 C      -0.269    3.429
    4471     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 319 CE2    -0.282    3.742
    4472     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 CZ     -0.292    3.752
    4473     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 CZ     -0.312    3.772
    4474     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B TYR 323 CD2    -0.317    3.437
    4475     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B MET 322 C      -0.325    3.445
    4476     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 OH     -0.327    3.587
    4477     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 OH     -0.330    3.440
    4478     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B MET 322 C      -0.334    3.914
    4479     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 319 CG     -0.349    3.809
    4480     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 OH     -0.353    3.613
    4481     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B TYR 323 CZ     -0.360    3.670
    4482     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B TYR 323 N      -0.378    3.023
    4483     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B MET 322 HB2    -0.382    2.992
    4484     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B GLU 363 OE2    -0.387    3.477
    4485     3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C  3U84.pdbqt #1/B MET 322 O      -0.399    3.759
    4486    
    4487 
    4488  
    4489 37 contacts 
    4490 
    4491 > hbonds :UNL showDist true radius 0.05 log true saveFile
    4492 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
    4493 > WRM-16.hbonds.txt
    4494    
    4495    
    4496     Finding intermodel H-bonds
    4497     Finding intramodel H-bonds
    4498     Constraints relaxed by 0.4 angstroms and 20 degrees
    4499     Models used:
    4500         1 3U84.pdbqt
    4501         2.1 3U84--WRM-16.result.pdbqt
    4502    
    4503     1 H-bonds
    4504     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    4505     3U84.pdbqt #1/B TRP 341 NE1  3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O  3U84.pdbqt #1/B TRP 341 HE1  3.103  2.136
    4506    
    4507 
    4508  
    4509 1 hydrogen bonds found 
    4510 
    4511 > select :UNL
    4512 
    4513 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4514 
    4515 > label sel text "Ligand "
    4516 
    4517 > label height 1
    4518 
    4519 > ~select
    4520 
    4521 Nothing selected 
    4522 
    4523 > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
    4524 > ypos .95
    4525 
    4526 > 2dlabels text "3U84 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    4527 
    4528 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
    4529 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    4530 > true
    4531 
    4532 > select :UNL
    4533 
    4534 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4535 
    4536 > view sel
    4537 
    4538 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
    4539 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    4540 > true
    4541 
    4542 > close
    4543 
    4544 > wait 5
    4545 
    4546 > set bgColor white
    4547 
    4548 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2YSM.pdbqt
    4549 
    4550 Chain information for 2YSM.pdbqt #1 
    4551 --- 
    4552 Chain | Description 
    4553 A | No description available 
    4554  
    4555 Opened 2YSM.pdbqt containing 1 structures (1584 atoms, 1601 bonds) 
    4556 
    4557 > wait 5
    4558 
    4559 > hide surfaces
    4560 
    4561 > hide atoms
    4562 
    4563 > show cartoons
    4564 
    4565 > wait 5
    4566 
    4567 > addh
    4568 
    4569 Summary of feedback from adding hydrogens to 2YSM.pdbqt #1 
    4570 --- 
    4571 notes | No usable SEQRES records for 2YSM.pdbqt (#1) chain A; guessing termini
    4572 instead 
    4573 Chain-initial residues that are actual N termini: /A GLY 1 
    4574 Chain-initial residues that are not actual N termini: 
    4575 Chain-final residues that are actual C termini: /A GLY 111 
    4576 Chain-final residues that are not actual C termini: 
    4577 29 hydrogen bonds 
    4578 15 hydrogens added 
    4579  
    4580 
    4581 > wait 5
    4582 
    4583 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--
    4584 > WRM-16.result.pdbqt
    4585 
    4586 Summary of feedback from opening
    4587 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--WRM-16.result.pdbqt 
    4588 --- 
    4589 warnings | Ignored bad PDB record found on line 2 
    4590 REMARK VINA RESULT: -7.5 0.000 0.000 
    4591  
    4592 Ignored bad PDB record found on line 3 
    4593 REMARK 5 active torsions: 
    4594  
    4595 Ignored bad PDB record found on line 4 
    4596 REMARK status: ('A' for Active; 'I' for Inactive) 
    4597  
    4598 Ignored bad PDB record found on line 5 
    4599 REMARK 1 A between atoms: C_9 and O_15 
    4600  
    4601 Ignored bad PDB record found on line 6 
    4602 REMARK 2 A between atoms: C_10 and O_17 
    4603  
    4604 184 messages similar to the above omitted 
    4605  
    4606 Opened 2YSM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4607 bonds) 
    4608 
    4609 > wait 5
    4610 
    4611 > close #2.2-9
    4612 
    4613 > wait 5
    4614 
    4615 > contacts :UNL radius 0.05 log true saveFile
    4616 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
    4617 > WRM-16.contacts.txt
    4618    
    4619    
    4620     Allowed overlap: -0.4
    4621     H-bond overlap reduction: 0.4
    4622     Ignore contacts between atoms separated by 4 bonds or less
    4623     Detect intra-residue contacts: False
    4624     Detect intra-molecule contacts: True
    4625    
    4626     58 contacts
    4627                       atom1                               atom2             overlap  distance
    4628     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 HG2    0.549    2.331
    4629     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A TRP 96 HB2    0.263    2.617
    4630     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 CG     0.262    3.318
    4631     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ILE 39 2HG1   0.200    2.560
    4632     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 H      0.194    2.566
    4633     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A ASN 94 CA     0.171    3.409
    4634     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A ASN 94 HA     0.167    2.713
    4635     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ILE 39 2HG1   0.075    2.685
    4636     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LEU 70 3HD2   0.068    2.692
    4637     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A PRO 52 HB3    0.066    2.814
    4638     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A TRP 96 CB     0.017    3.563
    4639     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LYS 55 HZ1    0.014    2.866
    4640     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A ASN 94 C      -0.022    3.602
    4641     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 2HG1   -0.039    2.919
    4642     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CG2    -0.053    3.633
    4643     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 HB     -0.053    2.933
    4644     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A ASN 94 N      -0.094    3.599
    4645     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 HB     -0.109    2.719
    4646     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A MET 69 O      -0.119    3.479
    4647     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 3HG1   -0.129    2.739
    4648     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LEU 70 3HD2   -0.130    2.890
    4649     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CB     -0.136    3.716
    4650     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 CB     -0.142    3.722
    4651     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 HB     -0.142    2.752
    4652     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A GLY 95 N      -0.146    3.651
    4653     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ILE 39 CG1    -0.151    3.611
    4654     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 O      -0.156    3.516
    4655     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 N      -0.158    3.543
    4656     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A PRO 92 O      -0.216    3.456
    4657     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 3HG1   -0.219    2.829
    4658     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CG1    -0.219    3.529
    4659     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A THR 93 C      -0.221    3.801
    4660     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LEU 70 CD2    -0.255    3.715
    4661     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LEU 70 CD2    -0.258    3.718
    4662     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ASP 76 OD1    -0.259    3.499
    4663     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 C      -0.264    3.844
    4664     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 2HG2   -0.266    3.146
    4665     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ILE 39 CG1    -0.271    3.731
    4666     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 2HG2   -0.280    2.890
    4667     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A PRO 52 CB     -0.282    3.862
    4668     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 2HG2   -0.286    2.896
    4669     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LEU 70 HA     -0.289    3.049
    4670     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ASP 73 OD1    -0.292    3.532
    4671     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 N      -0.297    3.802
    4672     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CG1    -0.297    3.877
    4673     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CG1    -0.299    3.609
    4674     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A PRO 92 HB2    -0.302    3.182
    4675     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 3HG1   -0.309    3.069
    4676     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A TRP 96 CB     -0.331    3.791
    4677     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 H      -0.335    3.215
    4678     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CB     -0.338    3.648
    4679     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LYS 45 HZ3    -0.358    3.118
    4680     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A PRO 92 HG2    -0.359    2.969
    4681     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A THR 93 O      -0.359    3.599
    4682     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2YSM.pdbqt #1/A TRP 96 N      -0.383    3.888
    4683     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A LYS 55 NZ     -0.384    3.889
    4684     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A VAL 71 CB     -0.385    3.695
    4685     2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C   2YSM.pdbqt #1/A ASP 76 OD1    -0.395    3.635
    4686    
    4687 
    4688  
    4689 58 contacts 
    4690 
    4691 > hbonds :UNL showDist true radius 0.05 log true saveFile
    4692 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
    4693 > WRM-16.hbonds.txt
    4694    
    4695    
    4696     Finding intermodel H-bonds
    4697     Finding intramodel H-bonds
    4698     Constraints relaxed by 0.4 angstroms and 20 degrees
    4699     Models used:
    4700         1 2YSM.pdbqt
    4701         2.1 2YSM--WRM-16.result.pdbqt
    4702    
    4703     0 H-bonds
    4704     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    4705    
    4706 
    4707  
    4708 0 hydrogen bonds found 
    4709 
    4710 > select :UNL
    4711 
    4712 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4713 
    4714 > label sel text "Ligand "
    4715 
    4716 > label height 1
    4717 
    4718 > ~select
    4719 
    4720 Nothing selected 
    4721 
    4722 > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
    4723 > ypos .95
    4724 
    4725 > 2dlabels text "2YSM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    4726 
    4727 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
    4728 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    4729 > true
    4730 
    4731 > select :UNL
    4732 
    4733 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4734 
    4735 > view sel
    4736 
    4737 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
    4738 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    4739 > true
    4740 
    4741 > close
    4742 
    4743 > wait 5
    4744 
    4745 > set bgColor white
    4746 
    4747 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LNK.pdbqt
    4748 
    4749 Chain information for 2LNK.pdbqt #1 
    4750 --- 
    4751 Chain | Description 
    4752 A B | No description available 
    4753 C | No description available 
    4754  
    4755 Opened 2LNK.pdbqt containing 1 structures (3899 atoms, 3931 bonds) 
    4756 
    4757 > wait 5
    4758 
    4759 > hide surfaces
    4760 
    4761 > hide atoms
    4762 
    4763 > show cartoons
    4764 
    4765 > wait 5
    4766 
    4767 > addh
    4768 
    4769 Summary of feedback from adding hydrogens to 2LNK.pdbqt #1 
    4770 --- 
    4771 notes | No usable SEQRES records for 2LNK.pdbqt (#1) chain A; guessing termini
    4772 instead 
    4773 No usable SEQRES records for 2LNK.pdbqt (#1) chain B; guessing termini instead 
    4774 No usable SEQRES records for 2LNK.pdbqt (#1) chain C; guessing termini instead 
    4775 Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C GLN
    4776 1897 
    4777 Chain-initial residues that are not actual N termini: 
    4778 Chain-final residues that are actual C termini: /A LYS 101, /B LYS 101, /C ALA
    4779 1935 
    4780 Chain-final residues that are not actual C termini: 
    4781 191 hydrogen bonds 
    4782 0 hydrogens added 
    4783  
    4784 
    4785 > wait 5
    4786 
    4787 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--
    4788 > WRM-16.result.pdbqt
    4789 
    4790 Summary of feedback from opening
    4791 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--WRM-16.result.pdbqt 
    4792 --- 
    4793 warnings | Ignored bad PDB record found on line 2 
    4794 REMARK VINA RESULT: -7.0 0.000 0.000 
    4795  
    4796 Ignored bad PDB record found on line 3 
    4797 REMARK 5 active torsions: 
    4798  
    4799 Ignored bad PDB record found on line 4 
    4800 REMARK status: ('A' for Active; 'I' for Inactive) 
    4801  
    4802 Ignored bad PDB record found on line 5 
    4803 REMARK 1 A between atoms: C_9 and O_15 
    4804  
    4805 Ignored bad PDB record found on line 6 
    4806 REMARK 2 A between atoms: C_10 and O_17 
    4807  
    4808 184 messages similar to the above omitted 
    4809  
    4810 Opened 2LNK--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4811 bonds) 
    4812 
    4813 > wait 5
    4814 
    4815 > close #2.2-9
    4816 
    4817 > wait 5
    4818 
    4819 > contacts :UNL radius 0.05 log true saveFile
    4820 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
    4821 > WRM-16.contacts.txt
    4822    
    4823    
    4824     Allowed overlap: -0.4
    4825     H-bond overlap reduction: 0.4
    4826     Ignore contacts between atoms separated by 4 bonds or less
    4827     Detect intra-residue contacts: False
    4828     Detect intra-molecule contacts: True
    4829    
    4830     34 contacts
    4831                      atom1                                atom2              overlap  distance
    4832     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 HD2      0.362    2.518
    4833     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 CD2      0.342    3.238
    4834     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A ASN 87 1HD2     0.261    2.349
    4835     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/C THR 1906 2HG2   0.132    2.628
    4836     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 HD2      0.076    2.534
    4837     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A GLU 88 HB2      0.041    2.379
    4838     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A ASN 87 ND2      0.005    3.230
    4839     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 HD2      -0.072    2.952
    4840     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A MET 84 SD       -0.095    3.637
    4841     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A MET 84 O        -0.109    3.049
    4842     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A ASN 87 ND2      -0.119    2.804
    4843     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A ASN 87 1HD2     -0.126    2.146
    4844     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/C THR 1906 CG2    -0.131    3.591
    4845     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CD1      -0.159    3.619
    4846     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A ASN 87 1HD2     -0.162    2.222
    4847     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 HD2      -0.219    2.829
    4848     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CD1      -0.222    3.682
    4849     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CZ       -0.228    3.688
    4850     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/A GLU 88 CB       -0.228    3.348
    4851     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 CD2      -0.254    3.564
    4852     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 CE2      -0.261    3.841
    4853     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A MET 84 HB3      -0.283    3.043
    4854     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A MET 84 SD       -0.288    3.830
    4855     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A ASN 87 ND2      -0.291    3.796
    4856     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CE1      -0.298    3.608
    4857     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 CD2      -0.300    3.880
    4858     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CE1      -0.300    3.760
    4859     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CE1      -0.318    3.778
    4860     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 72 HD2      -0.356    2.966
    4861     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O  2LNK.pdbqt #1/B PHE 27 CD2      -0.368    3.488
    4862     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CG       -0.376    3.836
    4863     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/B PHE 27 CE2      -0.386    3.846
    4864     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A MET 84 SD       -0.386    3.928
    4865     2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C  2LNK.pdbqt #1/A ASN 87 ND2      -0.390    3.895
    4866    
    4867 
    4868  
    4869 34 contacts 
    4870 
    4871 > hbonds :UNL showDist true radius 0.05 log true saveFile
    4872 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
    4873 > WRM-16.hbonds.txt
    4874    
    4875    
    4876     Finding intermodel H-bonds
    4877     Finding intramodel H-bonds
    4878     Constraints relaxed by 0.4 angstroms and 20 degrees
    4879     Models used:
    4880         1 2LNK.pdbqt
    4881         2.1 2LNK--WRM-16.result.pdbqt
    4882    
    4883     0 H-bonds
    4884     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    4885    
    4886 
    4887  
    4888 0 hydrogen bonds found 
    4889 
    4890 > select :UNL
    4891 
    4892 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4893 
    4894 > label sel text "Ligand "
    4895 
    4896 > label height 1
    4897 
    4898 > ~select
    4899 
    4900 Nothing selected 
    4901 
    4902 > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
    4903 > ypos .95
    4904 
    4905 > 2dlabels text "2LNK WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    4906 
    4907 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
    4908 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    4909 > true
    4910 
    4911 > select :UNL
    4912 
    4913 28 atoms, 31 bonds, 1 residue, 1 model selected 
    4914 
    4915 > view sel
    4916 
    4917 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
    4918 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    4919 > true
    4920 
    4921 > close
    4922 
    4923 > wait 5
    4924 
    4925 > set bgColor white
    4926 
    4927 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XUM.pdbqt
    4928 
    4929 Chain information for 1XUM.pdbqt #1 
    4930 --- 
    4931 Chain | Description 
    4932 A | No description available 
    4933  
    4934 Opened 1XUM.pdbqt containing 1 structures (2876 atoms, 2908 bonds) 
    4935 
    4936 > wait 5
    4937 
    4938 > hide surfaces
    4939 
    4940 > hide atoms
    4941 
    4942 > show cartoons
    4943 
    4944 > wait 5
    4945 
    4946 > addh
    4947 
    4948 Summary of feedback from adding hydrogens to 1XUM.pdbqt #1 
    4949 --- 
    4950 notes | No usable SEQRES records for 1XUM.pdbqt (#1) chain A; guessing termini
    4951 instead 
    4952 Chain-initial residues that are actual N termini: /A THR 54 
    4953 Chain-initial residues that are not actual N termini: 
    4954 Chain-final residues that are actual C termini: /A THR 236 
    4955 Chain-final residues that are not actual C termini: 
    4956 96 hydrogen bonds 
    4957 59 hydrogens added 
    4958  
    4959 
    4960 > wait 5
    4961 
    4962 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--
    4963 > WRM-16.result.pdbqt
    4964 
    4965 Summary of feedback from opening
    4966 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--WRM-16.result.pdbqt 
    4967 --- 
    4968 warnings | Ignored bad PDB record found on line 2 
    4969 REMARK VINA RESULT: -7.8 0.000 0.000 
    4970  
    4971 Ignored bad PDB record found on line 3 
    4972 REMARK 5 active torsions: 
    4973  
    4974 Ignored bad PDB record found on line 4 
    4975 REMARK status: ('A' for Active; 'I' for Inactive) 
    4976  
    4977 Ignored bad PDB record found on line 5 
    4978 REMARK 1 A between atoms: C_9 and O_15 
    4979  
    4980 Ignored bad PDB record found on line 6 
    4981 REMARK 2 A between atoms: C_10 and O_17 
    4982  
    4983 184 messages similar to the above omitted 
    4984  
    4985 Opened 1XUM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    4986 bonds) 
    4987 
    4988 > wait 5
    4989 
    4990 > close #2.2-9
    4991 
    4992 > wait 5
    4993 
    4994 > contacts :UNL radius 0.05 log true saveFile
    4995 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
    4996 > WRM-16.contacts.txt
    4997    
    4998    
    4999     Allowed overlap: -0.4
    5000     H-bond overlap reduction: 0.4
    5001     Ignore contacts between atoms separated by 4 bonds or less
    5002     Detect intra-residue contacts: False
    5003     Detect intra-molecule contacts: True
    5004    
    5005     50 contacts
    5006                      atom1                               atom2              overlap  distance
    5007     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A LYS 183 HD2    0.493    2.387
    5008     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 HG1    0.216    2.664
    5009     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A LYS 183 CD     0.190    3.390
    5010     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 206 CE2    0.101    3.359
    5011     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A SER 134 HG     0.100    2.660
    5012     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A LYS 183 HZ2    0.069    2.691
    5013     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A LYS 209 CD     0.018    3.102
    5014     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A LYS 209 CE     0.016    3.104
    5015     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 2HH1   -0.001    2.761
    5016     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A LYS 209 HD2    -0.002    2.422
    5017     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A ASP 160 OD2    -0.014    2.914
    5018     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 185 CB     -0.062    3.372
    5019     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 HG1    -0.100    2.980
    5020     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 OG1    -0.102    3.482
    5021     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ASN 110 2HD2   -0.109    2.869
    5022     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A GLU 157 OE1    -0.125    3.485
    5023     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 2HH1   -0.126    2.886
    5024     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 HD2    -0.128    2.888
    5025     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A LYS 183 NZ     -0.138    3.523
    5026     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 206 HE2    -0.140    2.900
    5027     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 206 CD2    -0.142    3.602
    5028     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 185 HB2    -0.156    2.766
    5029     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A GLU 157 CD     -0.190    3.770
    5030     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A TYR 185 HB2    -0.198    2.618
    5031     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A TYR 185 CD2    -0.208    3.368
    5032     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A LYS 209 HE1    -0.225    2.645
    5033     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 HD2    -0.234    2.994
    5034     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 CD     -0.246    3.706
    5035     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 NH1    -0.257    3.762
    5036     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A SER 134 OG     -0.264    3.524
    5037     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 206 CD2    -0.267    3.727
    5038     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ASN 110 ND2    -0.276    3.661
    5039     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 1HG2   -0.283    3.163
    5040     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 2HH1   -0.289    2.899
    5041     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A ASP 160 CG     -0.294    3.414
    5042     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ASN 186 ND2    -0.305    3.540
    5043     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 NH1    -0.309    3.694
    5044     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A TYR 185 CE2    -0.315    3.475
    5045     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A THR 159 OG1    -0.321    2.841
    5046     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 NH1    -0.331    3.716
    5047     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 NH1    -0.334    3.719
    5048     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 185 CG     -0.343    3.653
    5049     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 CG2    -0.352    3.932
    5050     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 NH1    -0.358    3.743
    5051     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A THR 159 HG1    -0.360    2.380
    5052     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A TYR 206 CE2    -0.371    3.831
    5053     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A SER 234 HG     -0.378    3.258
    5054     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A LYS 183 CE     -0.381    3.841
    5055     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A THR 159 OG1    -0.387    3.767
    5056     1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C  1XUM.pdbqt #1/A ARG 109 2HH1   -0.390    3.150
    5057    
    5058 
    5059  
    5060 50 contacts 
    5061 
    5062 > hbonds :UNL showDist true radius 0.05 log true saveFile
    5063 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
    5064 > WRM-16.hbonds.txt
    5065    
    5066    
    5067     Finding intermodel H-bonds
    5068     Finding intramodel H-bonds
    5069     Constraints relaxed by 0.4 angstroms and 20 degrees
    5070     Models used:
    5071         1 1XUM.pdbqt
    5072         2.1 1XUM--WRM-16.result.pdbqt
    5073    
    5074     2 H-bonds
    5075     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5076     1XUM.pdbqt #1/A ASN 186 ND2  1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A ASN 186 1HD2  3.170  2.565
    5077     1XUM.pdbqt #1/A ASN 208 ND2  1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O  1XUM.pdbqt #1/A ASN 208 2HD2  3.318  2.547
    5078    
    5079 
    5080  
    5081 2 hydrogen bonds found 
    5082 
    5083 > select :UNL
    5084 
    5085 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5086 
    5087 > label sel text "Ligand "
    5088 
    5089 > label height 1
    5090 
    5091 > ~select
    5092 
    5093 Nothing selected 
    5094 
    5095 > 2dlabels text "Binding Energy: -7.8 kcal/mol" color red size 18 xpos .03
    5096 > ypos .95
    5097 
    5098 > 2dlabels text "1XUM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    5099 
    5100 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
    5101 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    5102 > true
    5103 
    5104 > select :UNL
    5105 
    5106 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5107 
    5108 > view sel
    5109 
    5110 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
    5111 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    5112 > true
    5113 
    5114 > close
    5115 
    5116 > wait 5
    5117 
    5118 > set bgColor white
    5119 
    5120 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LTH.pdbqt
    5121 
    5122 Chain information for 6LTH.pdbqt #1 
    5123 --- 
    5124 Chain | Description 
    5125 I | No description available 
    5126 L | No description available 
    5127 M | No description available 
    5128 N | No description available 
    5129 O | No description available 
    5130 P | No description available 
    5131 Q | No description available 
    5132 R | No description available 
    5133  
    5134 Opened 6LTH.pdbqt containing 1 structures (30136 atoms, 30416 bonds) 
    5135 
    5136 > wait 5
    5137 
    5138 > hide surfaces
    5139 
    5140 > hide atoms
    5141 
    5142 > show cartoons
    5143 
    5144 > wait 5
    5145 
    5146 > addh
    5147 
    5148 Summary of feedback from adding hydrogens to 6LTH.pdbqt #1 
    5149 --- 
    5150 warnings | Not adding hydrogens to /M LYS 199 CD because it is missing heavy-
    5151 atom bond partners 
    5152 Not adding hydrogens to /M LYS 211 CG because it is missing heavy-atom bond
    5153 partners 
    5154 notes | No usable SEQRES records for 6LTH.pdbqt (#1) chain I; guessing termini
    5155 instead 
    5156 No usable SEQRES records for 6LTH.pdbqt (#1) chain L; guessing termini instead 
    5157 No usable SEQRES records for 6LTH.pdbqt (#1) chain M; guessing termini instead 
    5158 No usable SEQRES records for 6LTH.pdbqt (#1) chain N; guessing termini instead 
    5159 No usable SEQRES records for 6LTH.pdbqt (#1) chain O; guessing termini instead 
    5160 3 messages similar to the above omitted 
    5161 Chain-initial residues that are actual N termini: /I SER 350, /L ILE 1639, /M
    5162 SER 7, /N HIS 423, /O HIS 423, /P LYS 125, /Q SER 172, /R GLY 13 
    5163 Chain-initial residues that are not actual N termini: /I LEU 396, /L GLU 1802,
    5164 /L ILE 1954, /L GLU 2047, /L PRO 2225, /M ASP 78, /M ASP 172, /M GLN 257, /M
    5165 PRO 332, /N THR 602, /N ASN 671, /N LEU 858, /O THR 598, /O LEU 656, /O ALA
    5166 867, /P GLN 291, /P THR 399 
    5167 Chain-final residues that are actual C termini: /I LEU 476, /L SER 2285, /M
    5168 THR 357, /N GLN 952, /O GLN 952, /P GLU 505, /Q LEU 276, /R LYS 82 
    5169 Chain-final residues that are not actual C termini: /I LEU 388, /L ASP 1746,
    5170 /L LYS 1862, /L LYS 2025, /L GLN 2210, /M SER 67, /M ASP 101, /M PRO 249, /M
    5171 TYR 326, /N ASP 515, /N ARG 641, /N MET 703, /O GLN 545, /O ASP 651, /O ARG
    5172 717, /P LYS 177, /P GLU 369 
    5173 1386 hydrogen bonds 
    5174 Adding 'H' to /I LEU 396 
    5175 Adding 'H' to /L GLU 1802 
    5176 Adding 'H' to /L ILE 1954 
    5177 Adding 'H' to /L GLU 2047 
    5178 Adding 'H' to /M ASP 78 
    5179 10 messages similar to the above omitted 
    5180 /I LEU 388 is not terminus, removing H atom from 'C' 
    5181 /L ASP 1746 is not terminus, removing H atom from 'C' 
    5182 /L LYS 1862 is not terminus, removing H atom from 'C' 
    5183 /L LYS 2025 is not terminus, removing H atom from 'C' 
    5184 /L GLN 2210 is not terminus, removing H atom from 'C' 
    5185 12 messages similar to the above omitted 
    5186 -24 hydrogens added 
    5187  
    5188 
    5189 > wait 5
    5190 
    5191 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--
    5192 > WRM-16.result.pdbqt
    5193 
    5194 Summary of feedback from opening
    5195 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--WRM-16.result.pdbqt 
    5196 --- 
    5197 warnings | Ignored bad PDB record found on line 2 
    5198 REMARK VINA RESULT: -8.3 0.000 0.000 
    5199  
    5200 Ignored bad PDB record found on line 3 
    5201 REMARK 5 active torsions: 
    5202  
    5203 Ignored bad PDB record found on line 4 
    5204 REMARK status: ('A' for Active; 'I' for Inactive) 
    5205  
    5206 Ignored bad PDB record found on line 5 
    5207 REMARK 1 A between atoms: C_9 and O_15 
    5208  
    5209 Ignored bad PDB record found on line 6 
    5210 REMARK 2 A between atoms: C_10 and O_17 
    5211  
    5212 184 messages similar to the above omitted 
    5213  
    5214 Opened 6LTH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    5215 bonds) 
    5216 
    5217 > wait 5
    5218 
    5219 > close #2.2-9
    5220 
    5221 > wait 5
    5222 
    5223 > contacts :UNL radius 0.05 log true saveFile
    5224 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
    5225 > WRM-16.contacts.txt
    5226    
    5227    
    5228     Allowed overlap: -0.4
    5229     H-bond overlap reduction: 0.4
    5230     Ignore contacts between atoms separated by 4 bonds or less
    5231     Detect intra-residue contacts: False
    5232     Detect intra-molecule contacts: True
    5233    
    5234     48 contacts
    5235                       atom1                                atom2              overlap  distance
    5236     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 HG1     0.557    2.203
    5237     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 CG      0.147    3.313
    5238     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L PRO 2075 HG2    0.113    2.647
    5239     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L PHE 1999 HE1    0.078    2.342
    5240     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 HG1     0.071    2.689
    5241     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L TYR 2076 OH     0.045    3.215
    5242     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L GLN 2070 HA     0.021    2.399
    5243     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 HA      0.009    2.871
    5244     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LTH.pdbqt #1/L TYR 2076 CE1    0.003    3.577
    5245     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 CA      0.002    3.578
    5246     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLN 464 HG2     -0.053    2.813
    5247     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.064    2.824
    5248     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LTH.pdbqt #1/L TYR 2076 CZ     -0.085    3.665
    5249     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LTH.pdbqt #1/L PRO 2075 HB1    -0.087    2.967
    5250     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLN 464 CG      -0.091    3.551
    5251     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LTH.pdbqt #1/L TYR 2076 OH     -0.096    3.476
    5252     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.114    2.874
    5253     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L ASP 2072 HB1    -0.134    3.014
    5254     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.135    2.895
    5255     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 CB      -0.137    3.717
    5256     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L PRO 2075 HG2    -0.165    2.775
    5257     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLN 464 HG2     -0.175    2.785
    5258     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L GLN 2128 CD     -0.176    3.336
    5259     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.189    2.949
    5260     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLN 464 HB2     -0.190    2.950
    5261     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LTH.pdbqt #1/L PRO 2075 CB     -0.197    3.777
    5262     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 HB2     -0.207    3.087
    5263     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L GLN 2128 OE1    -0.214    3.304
    5264     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.215    2.825
    5265     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L PRO 2075 CG     -0.225    3.685
    5266     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L GLN 2070 CA     -0.232    3.352
    5267     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L PHE 1999 HE1    -0.235    2.845
    5268     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L GLN 2070 CD     -0.238    3.358
    5269     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLN 464 CG      -0.240    3.700
    5270     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 N       -0.245    3.750
    5271     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L ASP 2072 CB     -0.251    3.831
    5272     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L PHE 1999 CE1    -0.258    3.378
    5273     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I LYS 461 CG      -0.263    3.723
    5274     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L TYR 2076 CZ     -0.264    3.724
    5275     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L TYR 2076 HH     -0.283    3.043
    5276     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L GLN 2128 2HE2   -0.292    2.902
    5277     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L PHE 1999 HE1    -0.313    3.193
    5278     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 CG     -0.322    3.782
    5279     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L GLN 2070 NE2    -0.333    3.568
    5280     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 HG2    -0.349    2.959
    5281     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/I GLU 465 HG2     -0.380    3.140
    5282     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LTH.pdbqt #1/L GLN 2128 OE1    -0.393    3.333
    5283     6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LTH.pdbqt #1/L LYS 2003 CG     -0.397    3.857
    5284    
    5285 
    5286  
    5287 48 contacts 
    5288 
    5289 > hbonds :UNL showDist true radius 0.05 log true saveFile
    5290 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
    5291 > WRM-16.hbonds.txt
    5292    
    5293    
    5294     Finding intermodel H-bonds
    5295     Finding intramodel H-bonds
    5296     Constraints relaxed by 0.4 angstroms and 20 degrees
    5297     Models used:
    5298         1 6LTH.pdbqt
    5299         2.1 6LTH--WRM-16.result.pdbqt
    5300    
    5301     1 H-bonds
    5302     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5303     6LTH.pdbqt #1/L GLN 2128 NE2  6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O  6LTH.pdbqt #1/L GLN 2128 2HE2  3.227  2.606
    5304    
    5305 
    5306  
    5307 1 hydrogen bonds found 
    5308 
    5309 > select :UNL
    5310 
    5311 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5312 
    5313 > label sel text "Ligand "
    5314 
    5315 > label height 1
    5316 
    5317 > ~select
    5318 
    5319 Nothing selected 
    5320 
    5321 > 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
    5322 > ypos .95
    5323 
    5324 > 2dlabels text "6LTH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    5325 
    5326 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
    5327 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    5328 > true
    5329 
    5330 > select :UNL
    5331 
    5332 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5333 
    5334 > view sel
    5335 
    5336 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
    5337 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    5338 > true
    5339 
    5340 > close
    5341 
    5342 > wait 5
    5343 
    5344 > set bgColor white
    5345 
    5346 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3H9R.pdbqt
    5347 
    5348 Chain information for 3H9R.pdbqt #1 
    5349 --- 
    5350 Chain | Description 
    5351 A | No description available 
    5352 B | No description available 
    5353  
    5354 Opened 3H9R.pdbqt containing 1 structures (6620 atoms, 6691 bonds) 
    5355 
    5356 > wait 5
    5357 
    5358 > hide surfaces
    5359 
    5360 > hide atoms
    5361 
    5362 > show cartoons
    5363 
    5364 > wait 5
    5365 
    5366 > addh
    5367 
    5368 Summary of feedback from adding hydrogens to 3H9R.pdbqt #1 
    5369 --- 
    5370 warnings | Not adding hydrogens to /A ARG 218 CD because it is missing heavy-
    5371 atom bond partners 
    5372 Not adding hydrogens to /A SER 276 CB because it is missing heavy-atom bond
    5373 partners 
    5374 Not adding hydrogens to /A ASP 499 CB because it is missing heavy-atom bond
    5375 partners 
    5376 Not adding hydrogens to /B ARG 14 CB because it is missing heavy-atom bond
    5377 partners 
    5378 notes | No usable SEQRES records for 3H9R.pdbqt (#1) chain A; guessing termini
    5379 instead 
    5380 No usable SEQRES records for 3H9R.pdbqt (#1) chain B; guessing termini instead 
    5381 Chain-initial residues that are actual N termini: /A THR 172, /B GLY 2 
    5382 Chain-initial residues that are not actual N termini: /A SER 276, /A ARG 375 
    5383 Chain-final residues that are actual C termini: /A ASP 499, /B GLU 108 
    5384 Chain-final residues that are not actual C termini: /A SER 272, /A HIS 361 
    5385 360 hydrogen bonds 
    5386 Adding 'H' to /A SER 276 
    5387 Adding 'H' to /A ARG 375 
    5388 /A SER 272 is not terminus, removing H atom from 'C' 
    5389 /A HIS 361 is not terminus, removing H atom from 'C' 
    5390 7 hydrogens added 
    5391  
    5392 
    5393 > wait 5
    5394 
    5395 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--
    5396 > WRM-16.result.pdbqt
    5397 
    5398 Summary of feedback from opening
    5399 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--WRM-16.result.pdbqt 
    5400 --- 
    5401 warnings | Ignored bad PDB record found on line 2 
    5402 REMARK VINA RESULT: -10.1 0.000 0.000 
    5403  
    5404 Ignored bad PDB record found on line 3 
    5405 REMARK 5 active torsions: 
    5406  
    5407 Ignored bad PDB record found on line 4 
    5408 REMARK status: ('A' for Active; 'I' for Inactive) 
    5409  
    5410 Ignored bad PDB record found on line 5 
    5411 REMARK 1 A between atoms: C_9 and O_15 
    5412  
    5413 Ignored bad PDB record found on line 6 
    5414 REMARK 2 A between atoms: C_10 and O_17 
    5415  
    5416 184 messages similar to the above omitted 
    5417  
    5418 Opened 3H9R--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    5419 bonds) 
    5420 
    5421 > wait 5
    5422 
    5423 > close #2.2-9
    5424 
    5425 > wait 5
    5426 
    5427 > contacts :UNL radius 0.05 log true saveFile
    5428 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
    5429 > WRM-16.contacts.txt
    5430    
    5431    
    5432     Allowed overlap: -0.4
    5433     H-bond overlap reduction: 0.4
    5434     Ignore contacts between atoms separated by 4 bonds or less
    5435     Detect intra-residue contacts: False
    5436     Detect intra-molecule contacts: True
    5437    
    5438     56 contacts
    5439                       atom1                               atom2              overlap  distance
    5440     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A GLY 215 HA2    0.237    2.643
    5441     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3H9R.pdbqt #1/A LYS 340 HE1    0.199    2.681
    5442     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A SER 290 HG     0.131    2.629
    5443     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 HG1    0.091    2.669
    5444     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 OH     0.084    3.296
    5445     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 2HG1   0.026    2.734
    5446     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 3HD2   -0.001    2.611
    5447     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 CB     -0.040    3.500
    5448     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 HE1    -0.051    2.811
    5449     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 HE1    -0.053    2.663
    5450     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A GLY 215 CA     -0.076    3.656
    5451     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 2HD1   -0.077    2.687
    5452     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 O      -0.104    3.344
    5453     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 HH     -0.112    2.992
    5454     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 214 1HG2   -0.136    2.896
    5455     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 O      -0.146    3.506
    5456     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 HH     -0.154    2.914
    5457     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 2HG1   -0.157    2.767
    5458     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 3HD2   -0.158    2.768
    5459     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3H9R.pdbqt #1/A ASP 293 OD2    -0.168    3.528
    5460     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 CZ     -0.169    3.749
    5461     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 214 CG2    -0.171    3.631
    5462     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 285 CD1    -0.171    3.631
    5463     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A SER 290 OG     -0.174    3.434
    5464     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 CE     -0.180    3.640
    5465     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 3HD2   -0.205    2.815
    5466     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3H9R.pdbqt #1/A LYS 340 CE     -0.206    3.786
    5467     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 HE2    -0.256    3.016
    5468     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 CE2    -0.259    3.839
    5469     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 CG     -0.261    3.721
    5470     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O   3H9R.pdbqt #1/A LEU 343 2HD1   -0.276    2.736
    5471     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 CD2    -0.279    3.589
    5472     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O   3H9R.pdbqt #1/A ALA 353 HB1    -0.284    2.704
    5473     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 HG1    -0.287    3.047
    5474     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 HG1    -0.287    2.897
    5475     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 HB1    -0.289    3.049
    5476     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 HB2    -0.297    3.177
    5477     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 HB1    -0.298    3.058
    5478     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 343 CD2    -0.307    3.617
    5479     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3H9R.pdbqt #1/A TYR 292 CD2    -0.308    3.888
    5480     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 3HG2   -0.317    2.927
    5481     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 HB2    -0.319    3.079
    5482     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 285 CE1    -0.325    3.785
    5483     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3H9R.pdbqt #1/A TYR 292 HD2    -0.326    3.206
    5484     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 CB     -0.326    3.786
    5485     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 2HG1   -0.350    3.110
    5486     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 CG1    -0.350    3.810
    5487     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 CE2    -0.367    3.677
    5488     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 CE     -0.368    3.678
    5489     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 219 HE2    -0.371    2.981
    5490     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LYS 340 O      -0.374    3.464
    5491     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A ALA 233 CB     -0.376    3.956
    5492     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A LEU 263 1HD2   -0.382    3.262
    5493     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O   3H9R.pdbqt #1/A LEU 263 CD2    -0.384    3.544
    5494     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A TYR 285 HD1    -0.388    3.148
    5495     3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C   3H9R.pdbqt #1/A VAL 222 CG1    -0.390    3.970
    5496    
    5497 
    5498  
    5499 56 contacts 
    5500 
    5501 > hbonds :UNL showDist true radius 0.05 log true saveFile
    5502 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
    5503 > WRM-16.hbonds.txt
    5504    
    5505    
    5506     Finding intermodel H-bonds
    5507     Finding intramodel H-bonds
    5508     Constraints relaxed by 0.4 angstroms and 20 degrees
    5509     Models used:
    5510         1 3H9R.pdbqt
    5511         2.1 3H9R--WRM-16.result.pdbqt
    5512    
    5513     0 H-bonds
    5514     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5515    
    5516 
    5517  
    5518 0 hydrogen bonds found 
    5519 
    5520 > select :UNL
    5521 
    5522 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5523 
    5524 > label sel text "Ligand "
    5525 
    5526 > label height 1
    5527 
    5528 > ~select
    5529 
    5530 Nothing selected 
    5531 
    5532 > 2dlabels text "Binding Energy: -10.1 kcal/mol" color red size 18 xpos .03
    5533 > ypos .95
    5534 
    5535 > 2dlabels text "3H9R WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    5536 
    5537 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
    5538 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    5539 > true
    5540 
    5541 > select :UNL
    5542 
    5543 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5544 
    5545 > view sel
    5546 
    5547 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
    5548 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    5549 > true
    5550 
    5551 > close
    5552 
    5553 > wait 5
    5554 
    5555 > set bgColor white
    5556 
    5557 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1A5E.pdbqt
    5558 
    5559 Chain information for 1A5E.pdbqt #1 
    5560 --- 
    5561 Chain | Description 
    5562 A | No description available 
    5563  
    5564 Opened 1A5E.pdbqt containing 1 structures (2306 atoms, 2328 bonds) 
    5565 
    5566 > wait 5
    5567 
    5568 > hide surfaces
    5569 
    5570 > hide atoms
    5571 
    5572 > show cartoons
    5573 
    5574 > wait 5
    5575 
    5576 > addh
    5577 
    5578 Summary of feedback from adding hydrogens to 1A5E.pdbqt #1 
    5579 --- 
    5580 notes | No usable SEQRES records for 1A5E.pdbqt (#1) chain A; guessing termini
    5581 instead 
    5582 Chain-initial residues that are actual N termini: /A MET 1 
    5583 Chain-initial residues that are not actual N termini: 
    5584 Chain-final residues that are actual C termini: /A ASP 156 
    5585 Chain-final residues that are not actual C termini: 
    5586 64 hydrogen bonds 
    5587 0 hydrogens added 
    5588  
    5589 
    5590 > wait 5
    5591 
    5592 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--
    5593 > WRM-16.result.pdbqt
    5594 
    5595 Summary of feedback from opening
    5596 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--WRM-16.result.pdbqt 
    5597 --- 
    5598 warnings | Ignored bad PDB record found on line 2 
    5599 REMARK VINA RESULT: -6.6 0.000 0.000 
    5600  
    5601 Ignored bad PDB record found on line 3 
    5602 REMARK 5 active torsions: 
    5603  
    5604 Ignored bad PDB record found on line 4 
    5605 REMARK status: ('A' for Active; 'I' for Inactive) 
    5606  
    5607 Ignored bad PDB record found on line 5 
    5608 REMARK 1 A between atoms: C_9 and O_15 
    5609  
    5610 Ignored bad PDB record found on line 6 
    5611 REMARK 2 A between atoms: C_10 and O_17 
    5612  
    5613 184 messages similar to the above omitted 
    5614  
    5615 Opened 1A5E--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    5616 bonds) 
    5617 
    5618 > wait 5
    5619 
    5620 > close #2.2-9
    5621 
    5622 > wait 5
    5623 
    5624 > contacts :UNL radius 0.05 log true saveFile
    5625 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
    5626 > WRM-16.contacts.txt
    5627    
    5628    
    5629     Allowed overlap: -0.4
    5630     H-bond overlap reduction: 0.4
    5631     Ignore contacts between atoms separated by 4 bonds or less
    5632     Detect intra-residue contacts: False
    5633     Detect intra-molecule contacts: True
    5634    
    5635     45 contacts
    5636                       atom1                               atom2              overlap  distance
    5637     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 1HH1   0.185    2.695
    5638     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O   1A5E.pdbqt #1/A ARG 112 1HH1   0.171    1.889
    5639     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A GLY 111 HA3    0.148    2.732
    5640     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 HD3    0.134    2.626
    5641     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A LEU 117 2HD1   0.063    2.817
    5642     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A GLY 111 CA     0.033    3.547
    5643     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 NH1    0.030    3.475
    5644     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CD2    -0.013    3.593
    5645     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A LEU 117 CD1    -0.018    3.598
    5646     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.022    2.782
    5647     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CG     -0.036    3.616
    5648     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A PRO 151 HD3    -0.038    2.918
    5649     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.064    2.824
    5650     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CH2    -0.074    3.384
    5651     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.085    2.845
    5652     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O   1A5E.pdbqt #1/A ARG 112 NH1    -0.090    2.775
    5653     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O   1A5E.pdbqt #1/A LEU 117 3HD1   -0.118    2.538
    5654     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 87 NH2     -0.119    3.624
    5655     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.131    2.891
    5656     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A PRO 151 CD     -0.159    3.739
    5657     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.161    2.771
    5658     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CB     -0.174    3.634
    5659     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O   1A5E.pdbqt #1/A ASP 108 OD2    -0.193    3.133
    5660     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A GLY 111 N      -0.213    3.598
    5661     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CH2    -0.218    3.678
    5662     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CB     -0.221    3.681
    5663     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A GLY 111 N      -0.227    3.732
    5664     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 CD     -0.234    3.694
    5665     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CZ3    -0.255    3.565
    5666     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CD1    -0.273    3.853
    5667     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O   1A5E.pdbqt #1/A LEU 117 CD1    -0.275    3.395
    5668     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CE2    -0.277    3.857
    5669     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CZ3    -0.277    3.587
    5670     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CH2    -0.289    3.599
    5671     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 HD3    -0.299    3.059
    5672     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 HB3    -0.303    2.913
    5673     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A GLY 111 C      -0.323    3.783
    5674     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 1HH1   -0.339    2.949
    5675     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1A5E.pdbqt #1/A TRP 110 C      -0.352    3.932
    5676     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 HB2    -0.359    3.119
    5677     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 46 NH2     -0.361    3.746
    5678     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 87 2HH2    -0.361    3.241
    5679     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CD1    -0.370    3.830
    5680     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A TRP 110 CB     -0.386    3.846
    5681     1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C   1A5E.pdbqt #1/A ARG 112 1HH1   -0.399    3.009
    5682    
    5683 
    5684  
    5685 45 contacts 
    5686 
    5687 > hbonds :UNL showDist true radius 0.05 log true saveFile
    5688 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
    5689 > WRM-16.hbonds.txt
    5690    
    5691    
    5692     Finding intermodel H-bonds
    5693     Finding intramodel H-bonds
    5694     Constraints relaxed by 0.4 angstroms and 20 degrees
    5695     Models used:
    5696         1 1A5E.pdbqt
    5697         2.1 1A5E--WRM-16.result.pdbqt
    5698    
    5699     1 H-bonds
    5700     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5701     1A5E.pdbqt #1/A ARG 112 NH1  1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O  1A5E.pdbqt #1/A ARG 112 1HH1  2.775  1.889
    5702    
    5703 
    5704  
    5705 1 hydrogen bonds found 
    5706 
    5707 > select :UNL
    5708 
    5709 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5710 
    5711 > label sel text "Ligand "
    5712 
    5713 > label height 1
    5714 
    5715 > ~select
    5716 
    5717 Nothing selected 
    5718 
    5719 > 2dlabels text "Binding Energy: -6.6 kcal/mol" color red size 18 xpos .03
    5720 > ypos .95
    5721 
    5722 > 2dlabels text "1A5E WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    5723 
    5724 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
    5725 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    5726 > true
    5727 
    5728 > select :UNL
    5729 
    5730 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5731 
    5732 > view sel
    5733 
    5734 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
    5735 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    5736 > true
    5737 
    5738 > close
    5739 
    5740 > wait 5
    5741 
    5742 > set bgColor white
    5743 
    5744 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1ES7.pdbqt
    5745 
    5746 Chain information for 1ES7.pdbqt #1 
    5747 --- 
    5748 Chain | Description 
    5749 A C | No description available 
    5750 B | No description available 
    5751 D | No description available 
    5752  
    5753 Opened 1ES7.pdbqt containing 1 structures (5745 atoms, 5815 bonds) 
    5754 
    5755 > wait 5
    5756 
    5757 > hide surfaces
    5758 
    5759 > hide atoms
    5760 
    5761 > show cartoons
    5762 
    5763 > wait 5
    5764 
    5765 > addh
    5766 
    5767 Summary of feedback from adding hydrogens to 1ES7.pdbqt #1 
    5768 --- 
    5769 notes | No usable SEQRES records for 1ES7.pdbqt (#1) chain A; guessing termini
    5770 instead 
    5771 No usable SEQRES records for 1ES7.pdbqt (#1) chain B; guessing termini instead 
    5772 No usable SEQRES records for 1ES7.pdbqt (#1) chain C; guessing termini instead 
    5773 No usable SEQRES records for 1ES7.pdbqt (#1) chain D; guessing termini instead 
    5774 Chain-initial residues that are actual N termini: /A LYS 11, /B THR 232, /C
    5775 LYS 511, /D THR 732 
    5776 Chain-initial residues that are not actual N termini: /B GLU 270, /D GLU 770 
    5777 Chain-final residues that are actual C termini: /A ARG 114, /B PRO 317, /C ARG
    5778 614, /D ILE 820 
    5779 Chain-final residues that are not actual C termini: /B ASP 266, /D ASP 766 
    5780 270 hydrogen bonds 
    5781 Adding 'H' to /B GLU 270 
    5782 Adding 'H' to /D GLU 770 
    5783 /B ASP 266 is not terminus, removing H atom from 'C' 
    5784 /D ASP 766 is not terminus, removing H atom from 'C' 
    5785 28 hydrogens added 
    5786  
    5787 
    5788 > wait 5
    5789 
    5790 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--
    5791 > WRM-16.result.pdbqt
    5792 
    5793 Summary of feedback from opening
    5794 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--WRM-16.result.pdbqt 
    5795 --- 
    5796 warnings | Ignored bad PDB record found on line 2 
    5797 REMARK VINA RESULT: -7.5 0.000 0.000 
    5798  
    5799 Ignored bad PDB record found on line 3 
    5800 REMARK 5 active torsions: 
    5801  
    5802 Ignored bad PDB record found on line 4 
    5803 REMARK status: ('A' for Active; 'I' for Inactive) 
    5804  
    5805 Ignored bad PDB record found on line 5 
    5806 REMARK 1 A between atoms: C_9 and O_15 
    5807  
    5808 Ignored bad PDB record found on line 6 
    5809 REMARK 2 A between atoms: C_10 and O_17 
    5810  
    5811 184 messages similar to the above omitted 
    5812  
    5813 Opened 1ES7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    5814 bonds) 
    5815 
    5816 > wait 5
    5817 
    5818 > close #2.2-9
    5819 
    5820 > wait 5
    5821 
    5822 > contacts :UNL radius 0.05 log true saveFile
    5823 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
    5824 > WRM-16.contacts.txt
    5825    
    5826    
    5827     Allowed overlap: -0.4
    5828     H-bond overlap reduction: 0.4
    5829     Ignore contacts between atoms separated by 4 bonds or less
    5830     Detect intra-residue contacts: False
    5831     Detect intra-molecule contacts: True
    5832    
    5833     46 contacts
    5834                      atom1                               atom2             overlap  distance
    5835     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 HN    0.266    2.614
    5836     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ARG 16 HN     0.165    1.855
    5837     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B PRO 245 HB2   0.115    2.645
    5838     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 ND1    0.101    3.404
    5839     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 HD1    0.099    2.781
    5840     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A CYS 111 HN    0.038    2.022
    5841     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 HB2    -0.021    2.781
    5842     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 HB2    -0.077    2.687
    5843     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 N     -0.107    3.612
    5844     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 1HD2   -0.114    2.134
    5845     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B PRO 245 CB    -0.134    3.594
    5846     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A CYS 111 HN    -0.134    2.744
    5847     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ASN 56 1HD2   -0.156    2.766
    5848     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ARG 16 N      -0.177    2.822
    5849     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 HN     -0.181    2.791
    5850     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 CB    -0.198    3.658
    5851     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 HN     -0.206    2.966
    5852     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A GLY 110 HA1   -0.216    2.636
    5853     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 247 OD1   -0.230    3.470
    5854     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 OD2   -0.233    3.473
    5855     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 HB2    -0.234    2.994
    5856     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 CB     -0.239    3.699
    5857     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 HB2   -0.244    3.004
    5858     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 HB2    -0.248    3.128
    5859     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 246 HB2   -0.253    3.013
    5860     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A CYS 111 O     -0.274    3.364
    5861     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A GLY 110 CA    -0.280    3.400
    5862     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A CYS 111 O     -0.305    3.205
    5863     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 CB     -0.311    3.771
    5864     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 247 OD1   -0.316    3.556
    5865     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A LYS 15 CA     -0.326    3.446
    5866     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 O      -0.327    3.567
    5867     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 2HD2   -0.328    2.388
    5868     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A LYS 15 HA     -0.330    2.750
    5869     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 247 OD2   -0.331    3.571
    5870     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 CB     -0.338    3.648
    5871     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A CYS 111 N     -0.338    3.573
    5872     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A CYS 111 N     -0.339    3.024
    5873     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A CYS 111 O     -0.361    3.301
    5874     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ASN 56 ND2    -0.363    3.598
    5875     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A ARG 16 N      -0.363    3.748
    5876     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 ND2    -0.369    3.014
    5877     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/B ASP 247 CG    -0.374    3.834
    5878     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A HIS 54 HB2    -0.375    2.985
    5879     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 ND2    -0.381    3.066
    5880     1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C  1ES7.pdbqt #1/A CYS 111 HN    -0.394    3.274
    5881    
    5882 
    5883  
    5884 46 contacts 
    5885 
    5886 > hbonds :UNL showDist true radius 0.05 log true saveFile
    5887 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
    5888 > WRM-16.hbonds.txt
    5889    
    5890    
    5891     Finding intermodel H-bonds
    5892     Finding intramodel H-bonds
    5893     Constraints relaxed by 0.4 angstroms and 20 degrees
    5894     Models used:
    5895         1 1ES7.pdbqt
    5896         2.1 1ES7--WRM-16.result.pdbqt
    5897    
    5898     4 H-bonds
    5899     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5900     1ES7.pdbqt #1/A ARG 16 N    1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ARG 16 HN    2.822  1.855
    5901     1ES7.pdbqt #1/A ASN 56 ND2  1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 1HD2  3.014  2.134
    5902     1ES7.pdbqt #1/A ASN 56 ND2  1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A ASN 56 2HD2  3.066  2.388
    5903     1ES7.pdbqt #1/A CYS 111 N   1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O  1ES7.pdbqt #1/A CYS 111 HN   3.024  2.022
    5904    
    5905 
    5906  
    5907 4 hydrogen bonds found 
    5908 
    5909 > select :UNL
    5910 
    5911 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5912 
    5913 > label sel text "Ligand "
    5914 
    5915 > label height 1
    5916 
    5917 > ~select
    5918 
    5919 Nothing selected 
    5920 
    5921 > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
    5922 > ypos .95
    5923 
    5924 > 2dlabels text "1ES7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    5925 
    5926 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
    5927 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    5928 > true
    5929 
    5930 > select :UNL
    5931 
    5932 28 atoms, 31 bonds, 1 residue, 1 model selected 
    5933 
    5934 > view sel
    5935 
    5936 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
    5937 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    5938 > true
    5939 
    5940 > close
    5941 
    5942 > wait 5
    5943 
    5944 > set bgColor white
    5945 
    5946 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3TGX.pdbqt
    5947 
    5948 Chain information for 3TGX.pdbqt #1 
    5949 --- 
    5950 Chain | Description 
    5951 A M O | No description available 
    5952 B | No description available 
    5953 C G I K | No description available 
    5954 D | No description available 
    5955 E | No description available 
    5956 F | No description available 
    5957 H | No description available 
    5958 J | No description available 
    5959 L | No description available 
    5960 N | No description available 
    5961 P | No description available 
    5962  
    5963 Opened 3TGX.pdbqt containing 1 structures (41174 atoms, 41719 bonds) 
    5964 
    5965 > wait 5
    5966 
    5967 > hide surfaces
    5968 
    5969 > hide atoms
    5970 
    5971 > show cartoons
    5972 
    5973 > wait 5
    5974 
    5975 > addh
    5976 
    5977 Summary of feedback from adding hydrogens to 3TGX.pdbqt #1 
    5978 --- 
    5979 warning | Not adding hydrogens to /J ARG 126 CB because it is missing heavy-
    5980 atom bond partners 
    5981 notes | No usable SEQRES records for 3TGX.pdbqt (#1) chain A; guessing termini
    5982 instead 
    5983 No usable SEQRES records for 3TGX.pdbqt (#1) chain B; guessing termini instead 
    5984 No usable SEQRES records for 3TGX.pdbqt (#1) chain C; guessing termini instead 
    5985 No usable SEQRES records for 3TGX.pdbqt (#1) chain D; guessing termini instead 
    5986 No usable SEQRES records for 3TGX.pdbqt (#1) chain E; guessing termini instead 
    5987 11 messages similar to the above omitted 
    5988 Chain-initial residues that are actual N termini: /A CYS 1, /B GLY 2, /C CYS
    5989 1, /D GLY 2, /E CYS 1, /F GLY 2, /G CYS 1, /H ASP 4, /I CYS 1, /J GLY 2, /K
    5990 CYS 1, /L ASP 4, /M CYS 1, /N ASP 4, /O CYS 1, /P ASP 4 
    5991 Chain-initial residues that are not actual N termini: /B HIS 89, /D LEU 91, /F
    5992 THR 92, /H GLN 87, /J LEU 91, /L LEU 91, /N THR 92, /P THR 92 
    5993 Chain-final residues that are actual C termini: /A SER 208, /B LEU 123, /C GLU
    5994 209, /D LEU 123, /E GLN 207, /F LEU 123, /G GLU 209, /H LEU 123, /I GLU 209,
    5995 /J ARG 126, /K GLU 209, /L HIS 122, /M SER 208, /N HIS 120, /O SER 208, /P LEU
    5996 123 
    5997 Chain-final residues that are not actual C termini: /B THR 81, /D ARG 85, /F
    5998 ASN 82, /H ASN 82, /J THR 81, /L THR 81, /N THR 81, /P THR 81 
    5999 1792 hydrogen bonds 
    6000 Adding 'H' to /B HIS 89 
    6001 Adding 'H' to /D LEU 91 
    6002 Adding 'H' to /F THR 92 
    6003 Adding 'H' to /H GLN 87 
    6004 Adding 'H' to /J LEU 91 
    6005 3 messages similar to the above omitted 
    6006 /B THR 81 is not terminus, removing H atom from 'C' 
    6007 /D ARG 85 is not terminus, removing H atom from 'C' 
    6008 /F ASN 82 is not terminus, removing H atom from 'C' 
    6009 /H ASN 82 is not terminus, removing H atom from 'C' 
    6010 /J THR 81 is not terminus, removing H atom from 'C' 
    6011 3 messages similar to the above omitted 
    6012 80 hydrogens added 
    6013  
    6014 
    6015 > wait 5
    6016 
    6017 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--
    6018 > WRM-16.result.pdbqt
    6019 
    6020 Summary of feedback from opening
    6021 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--WRM-16.result.pdbqt 
    6022 --- 
    6023 warnings | Ignored bad PDB record found on line 2 
    6024 REMARK VINA RESULT: -8.5 0.000 0.000 
    6025  
    6026 Ignored bad PDB record found on line 3 
    6027 REMARK 5 active torsions: 
    6028  
    6029 Ignored bad PDB record found on line 4 
    6030 REMARK status: ('A' for Active; 'I' for Inactive) 
    6031  
    6032 Ignored bad PDB record found on line 5 
    6033 REMARK 1 A between atoms: C_9 and O_15 
    6034  
    6035 Ignored bad PDB record found on line 6 
    6036 REMARK 2 A between atoms: C_10 and O_17 
    6037  
    6038 184 messages similar to the above omitted 
    6039  
    6040 Opened 3TGX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    6041 bonds) 
    6042 
    6043 > wait 5
    6044 
    6045 > close #2.2-9
    6046 
    6047 > wait 5
    6048 
    6049 > contacts :UNL radius 0.05 log true saveFile
    6050 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
    6051 > WRM-16.contacts.txt
    6052    
    6053    
    6054     Allowed overlap: -0.4
    6055     H-bond overlap reduction: 0.4
    6056     Ignore contacts between atoms separated by 4 bonds or less
    6057     Detect intra-residue contacts: False
    6058     Detect intra-molecule contacts: True
    6059    
    6060     84 contacts
    6061                       atom1                               atom2             overlap  distance
    6062     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 1HD2   0.702    2.058
    6063     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M ASN 22 2HD2   0.553    2.327
    6064     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 HB2    0.512    2.368
    6065     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 ND2    0.484    2.901
    6066     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASP 81 OD1    0.349    3.011
    6067     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TYR 86 HH     0.297    2.463
    6068     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/E ALA 127 HB1   0.227    2.533
    6069     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 1HE2   0.207    2.403
    6070     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HG1    0.181    2.579
    6071     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 CB     0.180    3.400
    6072     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TYR 86 OH     0.166    3.094
    6073     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M ASN 22 ND2    0.163    3.342
    6074     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 CB     0.149    3.431
    6075     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TRP 21 CD1    0.133    3.447
    6076     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 NE     0.132    3.373
    6077     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 HB1    0.131    2.749
    6078     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TRP 21 HD1    0.115    2.765
    6079     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 CB     0.110    3.470
    6080     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB2    0.094    2.786
    6081     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ILE 66 CG1    0.089    3.491
    6082     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A GLN 82 HN     0.077    2.683
    6083     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/E ALA 127 CB    0.016    3.444
    6084     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TRP 21 NE1    0.005    3.500
    6085     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ILE 66 2HG1   0.001    2.879
    6086     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 2HD2   -0.001    2.611
    6087     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/E ALA 127 CB    -0.006    3.586
    6088     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASP 81 OD1    -0.008    3.248
    6089     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ILE 66 1HG1   -0.043    2.923
    6090     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A GLN 82 HN     -0.056    2.816
    6091     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TRP 21 HE1    -0.056    2.936
    6092     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M ASN 22 ND2    -0.057    3.292
    6093     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/M GLN 82 1HE2   -0.067    2.127
    6094     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 CG     -0.098    3.678
    6095     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 NE2    -0.104    3.339
    6096     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 ND2    -0.107    3.612
    6097     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ARG 65 HD2    -0.112    2.872
    6098     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 HB1    -0.119    2.879
    6099     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB1    -0.134    3.014
    6100     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/E ALA 127 HB1   -0.143    3.023
    6101     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 2HD2   -0.158    2.768
    6102     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M HIS 24 CG     -0.159    3.619
    6103     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HG1    -0.159    3.039
    6104     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/F ASN 62 HB2    -0.163    2.623
    6105     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 1HD2   -0.178    2.938
    6106     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 ND2    -0.185    3.690
    6107     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 CG     -0.188    3.648
    6108     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A GLN 82 N      -0.192    3.577
    6109     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB2    -0.208    2.818
    6110     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 2HD2   -0.228    3.108
    6111     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 HB2    -0.235    3.115
    6112     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 2HD2   -0.240    3.000
    6113     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M HIS 24 CE1    -0.248    3.708
    6114     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TYR 86 HH     -0.249    3.009
    6115     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 CG     -0.260    3.840
    6116     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 CB     -0.262    3.842
    6117     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 CD     -0.265    3.845
    6118     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 CZ     -0.271    3.851
    6119     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ILE 66 N      -0.274    3.779
    6120     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB1    -0.281    3.161
    6121     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/F ARG 65 HE     -0.296    3.176
    6122     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 HB2    -0.296    3.176
    6123     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 ND2    -0.298    3.533
    6124     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/A ASP 81 OD1    -0.308    3.248
    6125     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3TGX.pdbqt #1/E ALA 127 HB2   -0.313    3.193
    6126     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB2    -0.319    2.929
    6127     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M TYR 86 OH     -0.336    3.596
    6128     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ARG 65 CD     -0.339    3.799
    6129     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HB2    -0.343    2.953
    6130     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ARG 65 CB     -0.346    3.806
    6131     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 HG1    -0.347    3.107
    6132     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M HIS 24 CD2    -0.354    3.814
    6133     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/M GLN 82 HB2    -0.356    2.816
    6134     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ARG 65 HB2    -0.357    3.117
    6135     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 ND2    -0.361    3.746
    6136     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 2HD2   -0.361    3.121
    6137     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/M GLN 82 CG     -0.362    3.522
    6138     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/F ASN 62 ND2    -0.368    3.603
    6139     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A ASN 22 1HD2   -0.370    3.250
    6140     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 CB     -0.370    3.680
    6141     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M GLN 82 1HE2   -0.388    3.268
    6142     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M HIS 24 NE2    -0.389    3.774
    6143     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/A GLN 82 HB2    -0.390    3.150
    6144     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C   3TGX.pdbqt #1/M HIS 24 ND1    -0.394    3.779
    6145     3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O   3TGX.pdbqt #1/A ASN 22 ND2    -0.395    3.080
    6146    
    6147 
    6148  
    6149 84 contacts 
    6150 
    6151 > hbonds :UNL showDist true radius 0.05 log true saveFile
    6152 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
    6153 > WRM-16.hbonds.txt
    6154    
    6155    
    6156     Finding intermodel H-bonds
    6157     Finding intramodel H-bonds
    6158     Constraints relaxed by 0.4 angstroms and 20 degrees
    6159     Models used:
    6160         1 3TGX.pdbqt
    6161         2.1 3TGX--WRM-16.result.pdbqt
    6162    
    6163     1 H-bonds
    6164     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6165     3TGX.pdbqt #1/M GLN 82 NE2  3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O  3TGX.pdbqt #1/M GLN 82 1HE2  3.121  2.127
    6166    
    6167 
    6168  
    6169 1 hydrogen bonds found 
    6170 
    6171 > select :UNL
    6172 
    6173 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6174 
    6175 > label sel text "Ligand "
    6176 
    6177 > label height 1
    6178 
    6179 > ~select
    6180 
    6181 Nothing selected 
    6182 
    6183 > 2dlabels text "Binding Energy: -8.5 kcal/mol" color red size 18 xpos .03
    6184 > ypos .95
    6185 
    6186 > 2dlabels text "3TGX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    6187 
    6188 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
    6189 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    6190 > true
    6191 
    6192 > select :UNL
    6193 
    6194 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6195 
    6196 > view sel
    6197 
    6198 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
    6199 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    6200 > true
    6201 
    6202 > close
    6203 
    6204 > wait 5
    6205 
    6206 > set bgColor white
    6207 
    6208 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/4JUP.pdbqt
    6209 
    6210 Chain information for 4JUP.pdbqt #1 
    6211 --- 
    6212 Chain | Description 
    6213 A B | No description available 
    6214  
    6215 Opened 4JUP.pdbqt containing 1 structures (2664 atoms, 2690 bonds) 
    6216 
    6217 > wait 5
    6218 
    6219 > hide surfaces
    6220 
    6221 > hide atoms
    6222 
    6223 > show cartoons
    6224 
    6225 > wait 5
    6226 
    6227 > addh
    6228 
    6229 Summary of feedback from adding hydrogens to 4JUP.pdbqt #1 
    6230 --- 
    6231 notes | No usable SEQRES records for 4JUP.pdbqt (#1) chain A; guessing termini
    6232 instead 
    6233 No usable SEQRES records for 4JUP.pdbqt (#1) chain B; guessing termini instead 
    6234 Chain-initial residues that are actual N termini: /A LEU 22, /B LEU 22 
    6235 Chain-initial residues that are not actual N termini: /A ASN 71, /B ASN 71 
    6236 Chain-final residues that are actual C termini: /A GLY 108, /B GLY 108 
    6237 Chain-final residues that are not actual C termini: /A ALA 63, /B ALA 63 
    6238 116 hydrogen bonds 
    6239 Adding 'H' to /A ASN 71 
    6240 Adding 'H' to /B ASN 71 
    6241 /A ALA 63 is not terminus, removing H atom from 'C' 
    6242 /B ALA 63 is not terminus, removing H atom from 'C' 
    6243 -2 hydrogens added 
    6244  
    6245 
    6246 > wait 5
    6247 
    6248 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--
    6249 > WRM-16.result.pdbqt
    6250 
    6251 Summary of feedback from opening
    6252 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--WRM-16.result.pdbqt 
    6253 --- 
    6254 warnings | Ignored bad PDB record found on line 2 
    6255 REMARK VINA RESULT: -7.9 0.000 0.000 
    6256  
    6257 Ignored bad PDB record found on line 3 
    6258 REMARK 5 active torsions: 
    6259  
    6260 Ignored bad PDB record found on line 4 
    6261 REMARK status: ('A' for Active; 'I' for Inactive) 
    6262  
    6263 Ignored bad PDB record found on line 5 
    6264 REMARK 1 A between atoms: C_9 and O_15 
    6265  
    6266 Ignored bad PDB record found on line 6 
    6267 REMARK 2 A between atoms: C_10 and O_17 
    6268  
    6269 184 messages similar to the above omitted 
    6270  
    6271 Opened 4JUP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    6272 bonds) 
    6273 
    6274 > wait 5
    6275 
    6276 > close #2.2-9
    6277 
    6278 > wait 5
    6279 
    6280 > contacts :UNL radius 0.05 log true saveFile
    6281 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
    6282 > WRM-16.contacts.txt
    6283    
    6284    
    6285     Allowed overlap: -0.4
    6286     H-bond overlap reduction: 0.4
    6287     Ignore contacts between atoms separated by 4 bonds or less
    6288     Detect intra-residue contacts: False
    6289     Detect intra-molecule contacts: True
    6290    
    6291     77 contacts
    6292                       atom1                               atom2             overlap  distance
    6293     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B ASN 71 HA     0.493    1.967
    6294     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 HA     0.445    2.315
    6295     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 35 HB1    0.307    2.573
    6296     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HG     0.303    2.457
    6297     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 O      0.286    3.074
    6298     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 HB1    0.217    2.663
    6299     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 35 HD2    0.197    2.683
    6300     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B ASN 71 CA     0.183    2.977
    6301     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 HG2    0.161    2.599
    6302     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B HIS 31 CE1    0.142    3.018
    6303     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HG     0.130    2.630
    6304     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 2HH2   0.110    2.770
    6305     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 35 CB     0.083    3.497
    6306     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ILE 79 HA     0.074    2.686
    6307     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 CA     0.055    3.405
    6308     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 CG     0.047    3.413
    6309     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/A ARG 75 2HH2   0.027    1.993
    6310     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A THR 82 HG1    -0.010    2.770
    6311     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 HB1    -0.017    2.777
    6312     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HG     -0.018    2.778
    6313     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 2HH1   -0.024    2.634
    6314     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 NH2    -0.029    3.534
    6315     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 CB     -0.049    3.629
    6316     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 OG     -0.079    3.339
    6317     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A THR 82 HG1    -0.087    2.697
    6318     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  4JUP.pdbqt #1/A THR 82 HG1    -0.105    2.985
    6319     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 35 CD     -0.111    3.691
    6320     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ASN 71 HA     -0.119    2.999
    6321     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 OD2    -0.153    3.243
    6322     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/A ARG 75 NH2    -0.159    2.804
    6323     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 OD2    -0.165    3.255
    6324     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  4JUP.pdbqt #1/A THR 82 1HG2   -0.181    3.061
    6325     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A THR 82 OG1    -0.189    3.449
    6326     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 HA     -0.191    2.951
    6327     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 CE1    -0.199    3.779
    6328     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 30 HD2    -0.203    2.963
    6329     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 30 CD     -0.205    3.665
    6330     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ILE 79 1HG1   -0.205    2.965
    6331     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 2HH2   -0.206    2.816
    6332     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 NH1    -0.210    3.445
    6333     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 HG2    -0.213    2.973
    6334     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASN 71 2HD2   -0.213    3.093
    6335     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ILE 79 CA     -0.215    3.675
    6336     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HB1    -0.220    3.100
    6337     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  4JUP.pdbqt #1/A ILE 79 CG1    -0.228    3.808
    6338     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 OG     -0.243    3.503
    6339     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 CG     -0.244    3.824
    6340     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 2HH1   -0.246    2.856
    6341     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  4JUP.pdbqt #1/A ILE 79 1HG1   -0.248    3.128
    6342     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 OD2    -0.258    3.498
    6343     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ASN 71 OD1    -0.262    3.622
    6344     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 CB     -0.272    3.732
    6345     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B ASN 71 HB2    -0.297    2.717
    6346     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B ASN 71 CB     -0.302    3.422
    6347     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B HIS 31 ND1    -0.304    2.989
    6348     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASN 71 ND2    -0.305    3.810
    6349     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 C      -0.306    3.886
    6350     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/B ASN 71 CG     -0.306    3.426
    6351     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 CB     -0.308    3.768
    6352     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 C      -0.314    3.774
    6353     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 OG     -0.315    3.575
    6354     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 CG     -0.316    3.776
    6355     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 C      -0.326    3.786
    6356     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HG     -0.329    3.089
    6357     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B HIS 31 ND1    -0.343    3.848
    6358     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 OD1    -0.346    3.706
    6359     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 30 HG1    -0.355    3.115
    6360     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 NH2    -0.360    3.595
    6361     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ARG 35 CA     -0.362    3.942
    6362     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 CG     -0.365    3.675
    6363     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 HB1    -0.370    3.130
    6364     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B ASN 71 HA     -0.375    2.985
    6365     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O   4JUP.pdbqt #1/A ARG 75 CZ     -0.378    3.498
    6366     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 30 NH1    -0.384    3.769
    6367     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ASP 78 C      -0.385    3.845
    6368     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/B SER 34 CB     -0.388    3.698
    6369     4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C   4JUP.pdbqt #1/A ARG 75 2HH1   -0.396    3.276
    6370    
    6371 
    6372  
    6373 77 contacts 
    6374 
    6375 > hbonds :UNL showDist true radius 0.05 log true saveFile
    6376 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
    6377 > WRM-16.hbonds.txt
    6378    
    6379    
    6380     Finding intermodel H-bonds
    6381     Finding intramodel H-bonds
    6382     Constraints relaxed by 0.4 angstroms and 20 degrees
    6383     Models used:
    6384         1 4JUP.pdbqt
    6385         2.1 4JUP--WRM-16.result.pdbqt
    6386    
    6387     1 H-bonds
    6388     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6389     4JUP.pdbqt #1/A ARG 75 NH2  4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O  4JUP.pdbqt #1/A ARG 75 2HH2  2.804  1.993
    6390    
    6391 
    6392  
    6393 1 hydrogen bonds found 
    6394 
    6395 > select :UNL
    6396 
    6397 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6398 
    6399 > label sel text "Ligand "
    6400 
    6401 > label height 1
    6402 
    6403 > ~select
    6404 
    6405 Nothing selected 
    6406 
    6407 > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
    6408 > ypos .95
    6409 
    6410 > 2dlabels text "4JUP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    6411 
    6412 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
    6413 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    6414 > true
    6415 
    6416 > select :UNL
    6417 
    6418 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6419 
    6420 > view sel
    6421 
    6422 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
    6423 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    6424 > true
    6425 
    6426 > close
    6427 
    6428 > wait 5
    6429 
    6430 > set bgColor white
    6431 
    6432 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1FLI.pdbqt
    6433 
    6434 Chain information for 1FLI.pdbqt #1 
    6435 --- 
    6436 Chain | Description 
    6437 A | No description available 
    6438  
    6439 Opened 1FLI.pdbqt containing 1 structures (1589 atoms, 1612 bonds) 
    6440 
    6441 > wait 5
    6442 
    6443 > hide surfaces
    6444 
    6445 > hide atoms
    6446 
    6447 > show cartoons
    6448 
    6449 > wait 5
    6450 
    6451 > addh
    6452 
    6453 Summary of feedback from adding hydrogens to 1FLI.pdbqt #1 
    6454 --- 
    6455 notes | No usable SEQRES records for 1FLI.pdbqt (#1) chain A; guessing termini
    6456 instead 
    6457 Chain-initial residues that are actual N termini: /A PRO 276 
    6458 Chain-initial residues that are not actual N termini: 
    6459 Chain-final residues that are actual C termini: /A PRO 373 
    6460 Chain-final residues that are not actual C termini: 
    6461 38 hydrogen bonds 
    6462 1 hydrogens added 
    6463  
    6464 
    6465 > wait 5
    6466 
    6467 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--
    6468 > WRM-16.result.pdbqt
    6469 
    6470 Summary of feedback from opening
    6471 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--WRM-16.result.pdbqt 
    6472 --- 
    6473 warnings | Ignored bad PDB record found on line 2 
    6474 REMARK VINA RESULT: -7.4 0.000 0.000 
    6475  
    6476 Ignored bad PDB record found on line 3 
    6477 REMARK 5 active torsions: 
    6478  
    6479 Ignored bad PDB record found on line 4 
    6480 REMARK status: ('A' for Active; 'I' for Inactive) 
    6481  
    6482 Ignored bad PDB record found on line 5 
    6483 REMARK 1 A between atoms: C_9 and O_15 
    6484  
    6485 Ignored bad PDB record found on line 6 
    6486 REMARK 2 A between atoms: C_10 and O_17 
    6487  
    6488 184 messages similar to the above omitted 
    6489  
    6490 Opened 1FLI--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    6491 bonds) 
    6492 
    6493 > wait 5
    6494 
    6495 > close #2.2-9
    6496 
    6497 > wait 5
    6498 
    6499 > contacts :UNL radius 0.05 log true saveFile
    6500 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
    6501 > WRM-16.contacts.txt
    6502    
    6503    
    6504     Allowed overlap: -0.4
    6505     H-bond overlap reduction: 0.4
    6506     Ignore contacts between atoms separated by 4 bonds or less
    6507     Detect intra-residue contacts: False
    6508     Detect intra-molecule contacts: True
    6509    
    6510     45 contacts
    6511                       atom1                               atom2              overlap  distance
    6512     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PHE 309 HE1    0.444    2.316
    6513     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 1HD2   0.247    2.513
    6514     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 1HD2   0.080    2.680
    6515     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PHE 309 CE1    0.065    3.395
    6516     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 HB3    0.055    2.555
    6517     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CZ3    0.017    3.563
    6518     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 HB3    0.004    2.606
    6519     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PRO 371 HA     -0.026    2.786
    6520     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1FLI.pdbqt #1/A TRP 302 CD1    -0.029    3.609
    6521     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 HZ3    -0.038    2.918
    6522     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 CB     -0.055    3.515
    6523     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PRO 371 CA     -0.065    3.525
    6524     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1FLI.pdbqt #1/A TRP 302 CG     -0.089    3.669
    6525     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 CD2    -0.091    3.551
    6526     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 O      -0.144    3.384
    6527     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 2HD1   -0.165    2.925
    6528     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 CB     -0.166    3.476
    6529     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 HB3    -0.197    2.957
    6530     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 CD2    -0.206    3.666
    6531     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CH2    -0.224    3.684
    6532     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CZ3    -0.228    3.688
    6533     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 HH2    -0.228    2.838
    6534     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PRO 371 N      -0.247    3.632
    6535     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CE2    -0.250    3.710
    6536     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O   1FLI.pdbqt #1/A TRP 302 HH2    -0.251    2.671
    6537     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 369 C      -0.269    3.729
    6538     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O   1FLI.pdbqt #1/A SER 292 CB     -0.272    3.392
    6539     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 3HD2   -0.277    2.887
    6540     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CD2    -0.286    3.596
    6541     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 CD1    -0.287    3.747
    6542     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 3HD2   -0.291    2.901
    6543     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 CB     -0.294    3.604
    6544     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CE3    -0.311    3.771
    6545     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CZ2    -0.324    3.784
    6546     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CE3    -0.330    3.790
    6547     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 2HD1   -0.331    3.091
    6548     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A PHE 309 HE1    -0.348    3.108
    6549     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 CD1    -0.365    3.825
    6550     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CD2    -0.368    3.828
    6551     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A LEU 288 HB2    -0.373    3.133
    6552     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A TRP 302 CZ3    -0.388    3.698
    6553     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O   1FLI.pdbqt #1/A TRP 302 CH2    -0.390    3.550
    6554     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O   1FLI.pdbqt #1/A LEU 288 C      -0.393    3.553
    6555     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1FLI.pdbqt #1/A TRP 302 NE1    -0.396    3.901
    6556     1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C   1FLI.pdbqt #1/A GLN 370 C      -0.400    3.860
    6557    
    6558 
    6559  
    6560 45 contacts 
    6561 
    6562 > hbonds :UNL showDist true radius 0.05 log true saveFile
    6563 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
    6564 > WRM-16.hbonds.txt
    6565    
    6566    
    6567     Finding intermodel H-bonds
    6568     Finding intramodel H-bonds
    6569     Constraints relaxed by 0.4 angstroms and 20 degrees
    6570     Models used:
    6571         1 1FLI.pdbqt
    6572         2.1 1FLI--WRM-16.result.pdbqt
    6573    
    6574     0 H-bonds
    6575     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6576    
    6577 
    6578  
    6579 0 hydrogen bonds found 
    6580 
    6581 > select :UNL
    6582 
    6583 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6584 
    6585 > label sel text "Ligand "
    6586 
    6587 > label height 1
    6588 
    6589 > ~select
    6590 
    6591 Nothing selected 
    6592 
    6593 > 2dlabels text "Binding Energy: -7.4 kcal/mol" color red size 18 xpos .03
    6594 > ypos .95
    6595 
    6596 > 2dlabels text "1FLI WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    6597 
    6598 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
    6599 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    6600 > true
    6601 
    6602 > select :UNL
    6603 
    6604 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6605 
    6606 > view sel
    6607 
    6608 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
    6609 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    6610 > true
    6611 
    6612 > close
    6613 
    6614 > wait 5
    6615 
    6616 > set bgColor white
    6617 
    6618 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5LTY.pdbqt
    6619 
    6620 Chain information for 5LTY.pdbqt #1 
    6621 --- 
    6622 Chain | Description 
    6623 A B | No description available 
    6624 E F | No description available 
    6625 K | No description available 
    6626 M | No description available 
    6627  
    6628 Opened 5LTY.pdbqt containing 1 structures (4847 atoms, 5029 bonds) 
    6629 
    6630 > wait 5
    6631 
    6632 > hide surfaces
    6633 
    6634 > hide atoms
    6635 
    6636 > show cartoons
    6637 
    6638 > wait 5
    6639 
    6640 > addh
    6641 
    6642 Summary of feedback from adding hydrogens to 5LTY.pdbqt #1 
    6643 --- 
    6644 warnings | Not adding hydrogens to /A DT 1 P because it is missing heavy-atom
    6645 bond partners 
    6646 Not adding hydrogens to /B DT 1 P because it is missing heavy-atom bond
    6647 partners 
    6648 Not adding hydrogens to /F DG 19 P because it is missing heavy-atom bond
    6649 partners 
    6650 Not adding hydrogens to /E DG 19 P because it is missing heavy-atom bond
    6651 partners 
    6652 notes | No usable SEQRES records for 5LTY.pdbqt (#1) chain A; guessing termini
    6653 instead 
    6654 No usable SEQRES records for 5LTY.pdbqt (#1) chain B; guessing termini instead 
    6655 No usable SEQRES records for 5LTY.pdbqt (#1) chain E; guessing termini instead 
    6656 No usable SEQRES records for 5LTY.pdbqt (#1) chain F; guessing termini instead 
    6657 No usable SEQRES records for 5LTY.pdbqt (#1) chain K; guessing termini instead 
    6658 1 messages similar to the above omitted 
    6659 Chain-initial residues that are actual N termini: /A DT 1, /B DT 1, /E DG 19,
    6660 /F DG 19, /K THR 185, /M LYS 186 
    6661 Chain-initial residues that are not actual N termini: /A DG 12, /B DG 12, /E
    6662 DG 26, /F DG 26 
    6663 Chain-final residues that are actual C termini: /A DC 18, /B DC 18, /E DA 36,
    6664 /F DA 36, /K GLN 255, /M GLN 255 
    6665 Chain-final residues that are not actual C termini: /A DA 10, /B DA 10, /E DT
    6666 24, /F DT 24 
    6667 250 hydrogen bonds 
    6668 4 hydrogens added 
    6669  
    6670 
    6671 > wait 5
    6672 
    6673 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--
    6674 > WRM-16.result.pdbqt
    6675 
    6676 Summary of feedback from opening
    6677 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--WRM-16.result.pdbqt 
    6678 --- 
    6679 warnings | Ignored bad PDB record found on line 2 
    6680 REMARK VINA RESULT: -8.4 0.000 0.000 
    6681  
    6682 Ignored bad PDB record found on line 3 
    6683 REMARK 5 active torsions: 
    6684  
    6685 Ignored bad PDB record found on line 4 
    6686 REMARK status: ('A' for Active; 'I' for Inactive) 
    6687  
    6688 Ignored bad PDB record found on line 5 
    6689 REMARK 1 A between atoms: C_9 and O_15 
    6690  
    6691 Ignored bad PDB record found on line 6 
    6692 REMARK 2 A between atoms: C_10 and O_17 
    6693  
    6694 184 messages similar to the above omitted 
    6695  
    6696 Opened 5LTY--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    6697 bonds) 
    6698 
    6699 > wait 5
    6700 
    6701 > close #2.2-9
    6702 
    6703 > wait 5
    6704 
    6705 > contacts :UNL radius 0.05 log true saveFile
    6706 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
    6707 > WRM-16.contacts.txt
    6708    
    6709    
    6710     Allowed overlap: -0.4
    6711     H-bond overlap reduction: 0.4
    6712     Ignore contacts between atoms separated by 4 bonds or less
    6713     Detect intra-residue contacts: False
    6714     Detect intra-molecule contacts: True
    6715    
    6716     53 contacts
    6717                       atom1                               atom2             overlap  distance
    6718     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 243 HZ2   0.418    2.462
    6719     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DT 27 H73     0.241    2.639
    6720     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M ASN 236 HB1   0.235    2.645
    6721     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 243 NZ    0.227    3.278
    6722     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O   5LTY.pdbqt #1/E DA 28 H61     0.212    1.808
    6723     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 240 HB2   0.183    2.577
    6724     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M ASN 236 HB1   0.168    2.592
    6725     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 9 H71      0.135    2.625
    6726     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 H71      0.114    2.766
    6727     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 H72      0.090    2.670
    6728     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DA 28 H61     0.080    2.530
    6729     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 240 CB    0.033    3.427
    6730     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 H71      0.003    2.877
    6731     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DA 29 H61     -0.009    2.889
    6732     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DT 27 C7      -0.033    3.613
    6733     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O   5LTY.pdbqt #1/E DT 27 H73     -0.045    2.505
    6734     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 H72      -0.046    2.806
    6735     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 H72      -0.051    2.931
    6736     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M ASN 236 CB    -0.069    3.529
    6737     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M ASN 236 CB    -0.072    3.652
    6738     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 OP2      -0.079    3.459
    6739     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 9 C7       -0.099    3.559
    6740     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DT 27 H73     -0.100    2.710
    6741     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DT 27 H73     -0.122    3.002
    6742     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 240 HB2   -0.125    2.735
    6743     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 H72      -0.130    2.740
    6744     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 H72      -0.133    2.743
    6745     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M LYS 240 HB2   -0.145    3.025
    6746     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 C7       -0.147    3.727
    6747     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 O4       -0.148    3.508
    6748     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DA 29 N6      -0.149    3.654
    6749     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 C7       -0.153    3.613
    6750     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O   5LTY.pdbqt #1/E DA 28 N6      -0.168    2.813
    6751     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 C7       -0.179    3.489
    6752     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DA 28 N6      -0.183    3.418
    6753     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 C7       -0.193    3.503
    6754     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/B DT 9 C7       -0.198    3.778
    6755     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 C7       -0.209    3.669
    6756     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M ASN 236 C     -0.248    3.828
    6757     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 240 CG    -0.262    3.722
    6758     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/E DT 27 C7      -0.285    3.595
    6759     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 H71      -0.289    2.899
    6760     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M LYS 240 HD2   -0.299    3.179
    6761     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 H72      -0.302    2.912
    6762     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 H71      -0.305    3.185
    6763     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 7 C7       -0.311    3.891
    6764     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M ASN 236 O     -0.320    3.560
    6765     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O   5LTY.pdbqt #1/E DT 27 C5      -0.325    3.445
    6766     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/B DT 8 C7       -0.349    3.929
    6767     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M LYS 243 HZ3   -0.354    3.234
    6768     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5LTY.pdbqt #1/M ASN 236 O     -0.369    3.729
    6769     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O   5LTY.pdbqt #1/E DT 27 C7      -0.383    3.543
    6770     5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C   5LTY.pdbqt #1/M ASN 236 HB1   -0.396    3.006
    6771    
    6772 
    6773  
    6774 53 contacts 
    6775 
    6776 > hbonds :UNL showDist true radius 0.05 log true saveFile
    6777 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
    6778 > WRM-16.hbonds.txt
    6779    
    6780    
    6781     Finding intermodel H-bonds
    6782     Finding intramodel H-bonds
    6783     Constraints relaxed by 0.4 angstroms and 20 degrees
    6784     Models used:
    6785         1 5LTY.pdbqt
    6786         2.1 5LTY--WRM-16.result.pdbqt
    6787    
    6788     3 H-bonds
    6789     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6790     5LTY.pdbqt #1/E DA 28 N6  5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O  5LTY.pdbqt #1/E DA 28 H61  3.435  2.808
    6791     5LTY.pdbqt #1/E DA 28 N6  5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O  5LTY.pdbqt #1/E DA 28 H61  2.813  1.808
    6792     5LTY.pdbqt #1/E DA 28 N7  5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O  5LTY.pdbqt #1/E DA 28 H7   3.287  2.424
    6793    
    6794 
    6795  
    6796 3 hydrogen bonds found 
    6797 
    6798 > select :UNL
    6799 
    6800 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6801 
    6802 > label sel text "Ligand "
    6803 
    6804 > label height 1
    6805 
    6806 > ~select
    6807 
    6808 Nothing selected 
    6809 
    6810 > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
    6811 > ypos .95
    6812 
    6813 > 2dlabels text "5LTY WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    6814 
    6815 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
    6816 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    6817 > true
    6818 
    6819 > select :UNL
    6820 
    6821 28 atoms, 31 bonds, 1 residue, 1 model selected 
    6822 
    6823 > view sel
    6824 
    6825 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
    6826 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    6827 > true
    6828 
    6829 > close
    6830 
    6831 > wait 5
    6832 
    6833 > set bgColor white
    6834 
    6835 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1JDH.pdbqt
    6836 
    6837 Chain information for 1JDH.pdbqt #1 
    6838 --- 
    6839 Chain | Description 
    6840 A | No description available 
    6841 B | No description available 
    6842  
    6843 Opened 1JDH.pdbqt containing 1 structures (8191 atoms, 8243 bonds) 
    6844 
    6845 > wait 5
    6846 
    6847 > hide surfaces
    6848 
    6849 > hide atoms
    6850 
    6851 > show cartoons
    6852 
    6853 > wait 5
    6854 
    6855 > addh
    6856 
    6857 Summary of feedback from adding hydrogens to 1JDH.pdbqt #1 
    6858 --- 
    6859 warnings | Not adding hydrogens to /A ILE 140 CB because it is missing heavy-
    6860 atom bond partners 
    6861 Not adding hydrogens to /A ARG 151 CB because it is missing heavy-atom bond
    6862 partners 
    6863 Not adding hydrogens to /A LYS 158 CB because it is missing heavy-atom bond
    6864 partners 
    6865 Not adding hydrogens to /A GLU 163 CB because it is missing heavy-atom bond
    6866 partners 
    6867 Not adding hydrogens to /A GLN 177 CB because it is missing heavy-atom bond
    6868 partners 
    6869 28 messages similar to the above omitted 
    6870 notes | No usable SEQRES records for 1JDH.pdbqt (#1) chain A; guessing termini
    6871 instead 
    6872 No usable SEQRES records for 1JDH.pdbqt (#1) chain B; guessing termini instead 
    6873 Chain-initial residues that are actual N termini: /A ALA 135, /B LEU 12 
    6874 Chain-initial residues that are not actual N termini: /A ARG 151, /A PHE 560 
    6875 Chain-final residues that are actual C termini: /A SER 663, /B VAL 49 
    6876 Chain-final residues that are not actual C termini: /A ILE 140, /A GLN 548 
    6877 502 hydrogen bonds 
    6878 Adding 'H' to /A ARG 151 
    6879 Adding 'H' to /A PHE 560 
    6880 /A ILE 140 is not terminus, removing H atom from 'C' 
    6881 /A GLN 548 is not terminus, removing H atom from 'C' 
    6882 5 hydrogens added 
    6883  
    6884 
    6885 > wait 5
    6886 
    6887 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--
    6888 > WRM-16.result.pdbqt
    6889 
    6890 Summary of feedback from opening
    6891 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--WRM-16.result.pdbqt 
    6892 --- 
    6893 warnings | Ignored bad PDB record found on line 2 
    6894 REMARK VINA RESULT: -6.7 0.000 0.000 
    6895  
    6896 Ignored bad PDB record found on line 3 
    6897 REMARK 5 active torsions: 
    6898  
    6899 Ignored bad PDB record found on line 4 
    6900 REMARK status: ('A' for Active; 'I' for Inactive) 
    6901  
    6902 Ignored bad PDB record found on line 5 
    6903 REMARK 1 A between atoms: C_9 and O_15 
    6904  
    6905 Ignored bad PDB record found on line 6 
    6906 REMARK 2 A between atoms: C_10 and O_17 
    6907  
    6908 184 messages similar to the above omitted 
    6909  
    6910 Opened 1JDH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    6911 bonds) 
    6912 
    6913 > wait 5
    6914 
    6915 > close #2.2-9
    6916 
    6917 > wait 5
    6918 
    6919 > contacts :UNL radius 0.05 log true saveFile
    6920 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
    6921 > WRM-16.contacts.txt
    6922    
    6923    
    6924     Allowed overlap: -0.4
    6925     H-bond overlap reduction: 0.4
    6926     Ignore contacts between atoms separated by 4 bonds or less
    6927     Detect intra-residue contacts: False
    6928     Detect intra-molecule contacts: True
    6929    
    6930     49 contacts
    6931                       atom1                               atom2              overlap  distance
    6932     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A VAL 168 2HG1   0.358    2.522
    6933     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 HE     0.338    2.542
    6934     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 HE     0.255    1.805
    6935     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A GLU 163 HA     0.243    2.517
    6936     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1JDH.pdbqt #1/A GLU 163 HA     0.123    2.757
    6937     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 HB2    0.103    2.357
    6938     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A VAL 168 3HG2   0.097    2.783
    6939     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 HB2    0.055    2.555
    6940     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A VAL 168 CG1    0.046    3.534
    6941     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1JDH.pdbqt #1/A GLU 163 CA     0.013    3.567
    6942     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 NE     0.003    3.502
    6943     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1JDH.pdbqt #1/A GLU 163 CB     -0.018    3.598
    6944     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A THR 201 HA     -0.027    2.487
    6945     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 CB     -0.038    3.198
    6946     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 2HH2   -0.088    2.968
    6947     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 HB1    -0.090    2.850
    6948     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 ND2    -0.106    3.611
    6949     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A GLN 165 1HE2   -0.115    2.995
    6950     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 NE     -0.118    2.803
    6951     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ASN 161 HA     -0.118    2.538
    6952     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 1HD2   -0.126    2.736
    6953     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A VAL 168 CG2    -0.146    3.726
    6954     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 HB2    -0.155    3.035
    6955     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A GLU 163 CA     -0.159    3.619
    6956     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A GLU 163 HA     -0.171    2.781
    6957     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 CB     -0.177    3.487
    6958     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 CB     -0.204    3.664
    6959     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1JDH.pdbqt #1/A GLU 163 HB2    -0.206    3.086
    6960     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 1HD2   -0.213    2.823
    6961     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A THR 201 OG1    -0.218    2.738
    6962     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASP 162 O      -0.235    3.475
    6963     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 CB     -0.251    3.561
    6964     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 NH2    -0.267    3.772
    6965     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ASN 161 CA     -0.284    3.404
    6966     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A GLN 165 OE1    -0.287    3.647
    6967     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 HE     -0.295    3.175
    6968     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 161 O      -0.303    3.543
    6969     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 ND2    -0.310    3.545
    6970     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 CZ     -0.336    3.496
    6971     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 HB1    -0.340    2.950
    6972     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 HE     -0.356    2.966
    6973     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1JDH.pdbqt #1/A GLU 163 O      -0.363    3.723
    6974     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A LEU 160 O      -0.365    3.725
    6975     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 HB1    -0.368    3.128
    6976     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ASN 204 ND2    -0.369    3.604
    6977     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A THR 201 2HG2   -0.380    3.260
    6978     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A THR 201 CA     -0.385    3.545
    6979     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C   1JDH.pdbqt #1/A ARG 200 CB     -0.389    3.969
    6980     1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O   1JDH.pdbqt #1/A ARG 200 2HH2   -0.395    2.415
    6981    
    6982 
    6983  
    6984 49 contacts 
    6985 
    6986 > hbonds :UNL showDist true radius 0.05 log true saveFile
    6987 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
    6988 > WRM-16.hbonds.txt
    6989    
    6990    
    6991     Finding intermodel H-bonds
    6992     Finding intramodel H-bonds
    6993     Constraints relaxed by 0.4 angstroms and 20 degrees
    6994     Models used:
    6995         1 1JDH.pdbqt
    6996         2.1 1JDH--WRM-16.result.pdbqt
    6997    
    6998     4 H-bonds
    6999     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7000     1JDH.pdbqt #1/A ASN 161 ND2  1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O  1JDH.pdbqt #1/A ASN 161 1HD2  3.118  2.516
    7001     1JDH.pdbqt #1/A ARG 200 NE   1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O  1JDH.pdbqt #1/A ARG 200 HE    2.803  1.805
    7002     1JDH.pdbqt #1/A ARG 200 NH2  1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O  1JDH.pdbqt #1/A ARG 200 2HH2  3.325  2.546
    7003     1JDH.pdbqt #1/A ARG 200 NH2  1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O  1JDH.pdbqt #1/A ARG 200 2HH2  3.343  2.415
    7004    
    7005 
    7006  
    7007 4 hydrogen bonds found 
    7008 
    7009 > select :UNL
    7010 
    7011 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7012 
    7013 > label sel text "Ligand "
    7014 
    7015 > label height 1
    7016 
    7017 > ~select
    7018 
    7019 Nothing selected 
    7020 
    7021 > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
    7022 > ypos .95
    7023 
    7024 > 2dlabels text "1JDH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    7025 
    7026 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
    7027 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    7028 > true
    7029 
    7030 > select :UNL
    7031 
    7032 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7033 
    7034 > view sel
    7035 
    7036 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
    7037 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    7038 > true
    7039 
    7040 > close
    7041 
    7042 > wait 5
    7043 
    7044 > set bgColor white
    7045 
    7046 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LZP.pdbqt
    7047 
    7048 Chain information for 6LZP.pdbqt #1 
    7049 --- 
    7050 Chain | Description 
    7051 A | No description available 
    7052  
    7053 Opened 6LZP.pdbqt containing 1 structures (1381 atoms, 1395 bonds) 
    7054 
    7055 > wait 5
    7056 
    7057 > hide surfaces
    7058 
    7059 > hide atoms
    7060 
    7061 > show cartoons
    7062 
    7063 > wait 5
    7064 
    7065 > addh
    7066 
    7067 Summary of feedback from adding hydrogens to 6LZP.pdbqt #1 
    7068 --- 
    7069 notes | No usable SEQRES records for 6LZP.pdbqt (#1) chain A; guessing termini
    7070 instead 
    7071 Chain-initial residues that are actual N termini: /A HIS 171 
    7072 Chain-initial residues that are not actual N termini: 
    7073 Chain-final residues that are actual C termini: /A SER 258 
    7074 Chain-final residues that are not actual C termini: 
    7075 35 hydrogen bonds 
    7076 1 hydrogens added 
    7077  
    7078 
    7079 > wait 5
    7080 
    7081 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--
    7082 > WRM-16.result.pdbqt
    7083 
    7084 Summary of feedback from opening
    7085 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--WRM-16.result.pdbqt 
    7086 --- 
    7087 warnings | Ignored bad PDB record found on line 2 
    7088 REMARK VINA RESULT: -6.5 0.000 0.000 
    7089  
    7090 Ignored bad PDB record found on line 3 
    7091 REMARK 5 active torsions: 
    7092  
    7093 Ignored bad PDB record found on line 4 
    7094 REMARK status: ('A' for Active; 'I' for Inactive) 
    7095  
    7096 Ignored bad PDB record found on line 5 
    7097 REMARK 1 A between atoms: C_9 and O_15 
    7098  
    7099 Ignored bad PDB record found on line 6 
    7100 REMARK 2 A between atoms: C_10 and O_17 
    7101  
    7102 184 messages similar to the above omitted 
    7103  
    7104 Opened 6LZP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    7105 bonds) 
    7106 
    7107 > wait 5
    7108 
    7109 > close #2.2-9
    7110 
    7111 > wait 5
    7112 
    7113 > contacts :UNL radius 0.05 log true saveFile
    7114 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
    7115 > WRM-16.contacts.txt
    7116    
    7117    
    7118     Allowed overlap: -0.4
    7119     H-bond overlap reduction: 0.4
    7120     Ignore contacts between atoms separated by 4 bonds or less
    7121     Detect intra-residue contacts: False
    7122     Detect intra-molecule contacts: True
    7123    
    7124     42 contacts
    7125                       atom1                               atom2             overlap  distance
    7126     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A TRP 206 HE3   0.364    2.516
    7127     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 HG2   0.319    2.441
    7128     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PHE 204 HE1   0.260    2.620
    7129     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A TRP 206 CE3   0.181    3.399
    7130     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PRO 215 HA    0.168    2.712
    7131     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 HE2   0.150    2.460
    7132     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PRO 215 CA    0.145    3.435
    7133     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PHE 204 CE1   0.125    3.455
    7134     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PRO 215 N     0.050    3.455
    7135     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 HE1   0.040    2.840
    7136     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LZP.pdbqt #1/A THR 205 H     0.034    1.986
    7137     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A THR 205 H     -0.009    2.619
    7138     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 204 HE1   -0.027    2.637
    7139     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 CG    -0.029    3.489
    7140     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A THR 214 C     -0.067    3.647
    7141     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A THR 205 HG1   -0.077    2.687
    7142     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 204 HB2   -0.091    2.701
    7143     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 HG2   -0.093    2.703
    7144     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 HB2   -0.114    2.874
    7145     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 HE2   -0.120    2.880
    7146     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A TRP 206 CZ3   -0.132    3.712
    7147     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LZP.pdbqt #1/A THR 205 HG1   -0.139    2.159
    7148     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 HG2   -0.146    2.906
    7149     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 CE2   -0.174    3.484
    7150     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LZP.pdbqt #1/A THR 205 O     -0.176    3.116
    7151     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 HE2   -0.179    2.789
    7152     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 204 HE1   -0.191    2.951
    7153     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 CE    -0.193    3.773
    7154     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 204 CE1   -0.195    3.505
    7155     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 HE2   -0.234    2.844
    7156     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 204 CB    -0.256    3.836
    7157     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 CE2   -0.256    3.566
    7158     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A THR 205 N     -0.271    3.506
    7159     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A TRP 206 HE3   -0.271    3.031
    7160     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 CB    -0.294    3.754
    7161     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A MET 213 CG    -0.298    3.758
    7162     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PRO 215 CB    -0.314    3.894
    7163     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O   6LZP.pdbqt #1/A THR 205 N     -0.320    2.965
    7164     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A TRP 206 HZ3   -0.324    3.204
    7165     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL  6LZP.pdbqt #1/A PHE 204 CZ    -0.337    3.917
    7166     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A THR 205 OG1   -0.354    3.464
    7167     6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C   6LZP.pdbqt #1/A PHE 218 CE2   -0.361    3.821
    7168    
    7169 
    7170  
    7171 42 contacts 
    7172 
    7173 > hbonds :UNL showDist true radius 0.05 log true saveFile
    7174 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
    7175 > WRM-16.hbonds.txt
    7176    
    7177    
    7178     Finding intermodel H-bonds
    7179     Finding intramodel H-bonds
    7180     Constraints relaxed by 0.4 angstroms and 20 degrees
    7181     Models used:
    7182         1 6LZP.pdbqt
    7183         2.1 6LZP--WRM-16.result.pdbqt
    7184    
    7185     2 H-bonds
    7186     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7187     6LZP.pdbqt #1/A THR 205 N    6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O  6LZP.pdbqt #1/A THR 205 H    2.965  1.986
    7188     6LZP.pdbqt #1/A THR 205 OG1  6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O  6LZP.pdbqt #1/A THR 205 HG1  3.071  2.159
    7189    
    7190 
    7191  
    7192 2 hydrogen bonds found 
    7193 
    7194 > select :UNL
    7195 
    7196 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7197 
    7198 > label sel text "Ligand "
    7199 
    7200 > label height 1
    7201 
    7202 > ~select
    7203 
    7204 Nothing selected 
    7205 
    7206 > 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
    7207 > ypos .95
    7208 
    7209 > 2dlabels text "6LZP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    7210 
    7211 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
    7212 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    7213 > true
    7214 
    7215 > select :UNL
    7216 
    7217 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7218 
    7219 > view sel
    7220 
    7221 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
    7222 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    7223 > true
    7224 
    7225 > close
    7226 
    7227 > wait 5
    7228 
    7229 > set bgColor white
    7230 
    7231 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CS1.pdbqt
    7232 
    7233 Chain information for 2CS1.pdbqt #1 
    7234 --- 
    7235 Chain | Description 
    7236 A | No description available 
    7237  
    7238 Opened 2CS1.pdbqt containing 1 structures (1441 atoms, 1451 bonds) 
    7239 
    7240 > wait 5
    7241 
    7242 > hide surfaces
    7243 
    7244 > hide atoms
    7245 
    7246 > show cartoons
    7247 
    7248 > wait 5
    7249 
    7250 > addh
    7251 
    7252 Summary of feedback from adding hydrogens to 2CS1.pdbqt #1 
    7253 --- 
    7254 notes | No usable SEQRES records for 2CS1.pdbqt (#1) chain A; guessing termini
    7255 instead 
    7256 Chain-initial residues that are actual N termini: /A GLY 1 
    7257 Chain-initial residues that are not actual N termini: 
    7258 Chain-final residues that are actual C termini: /A GLY 92 
    7259 Chain-final residues that are not actual C termini: 
    7260 43 hydrogen bonds 
    7261 1 hydrogens added 
    7262  
    7263 
    7264 > wait 5
    7265 
    7266 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--
    7267 > WRM-16.result.pdbqt
    7268 
    7269 Summary of feedback from opening
    7270 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--WRM-16.result.pdbqt 
    7271 --- 
    7272 warnings | Ignored bad PDB record found on line 2 
    7273 REMARK VINA RESULT: -7.0 0.000 0.000 
    7274  
    7275 Ignored bad PDB record found on line 3 
    7276 REMARK 5 active torsions: 
    7277  
    7278 Ignored bad PDB record found on line 4 
    7279 REMARK status: ('A' for Active; 'I' for Inactive) 
    7280  
    7281 Ignored bad PDB record found on line 5 
    7282 REMARK 1 A between atoms: C_9 and O_15 
    7283  
    7284 Ignored bad PDB record found on line 6 
    7285 REMARK 2 A between atoms: C_10 and O_17 
    7286  
    7287 184 messages similar to the above omitted 
    7288  
    7289 Opened 2CS1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    7290 bonds) 
    7291 
    7292 > wait 5
    7293 
    7294 > close #2.2-9
    7295 
    7296 > wait 5
    7297 
    7298 > contacts :UNL radius 0.05 log true saveFile
    7299 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
    7300 > WRM-16.contacts.txt
    7301    
    7302    
    7303     Allowed overlap: -0.4
    7304     H-bond overlap reduction: 0.4
    7305     Ignore contacts between atoms separated by 4 bonds or less
    7306     Detect intra-residue contacts: False
    7307     Detect intra-molecule contacts: True
    7308    
    7309     50 contacts
    7310                       atom1                               atom2             overlap  distance
    7311     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A ALA 14 HB2    0.371    2.389
    7312     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CS1.pdbqt #1/A SER 13 HG     0.226    1.834
    7313     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A ALA 61 HB1    0.195    2.685
    7314     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 HD2    0.150    2.610
    7315     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 HG2    0.131    2.629
    7316     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 HG2    0.080    2.680
    7317     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LYS 10 HD2    0.072    2.688
    7318     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A ALA 14 CB     0.013    3.447
    7319     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 CD1    -0.019    3.599
    7320     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 HG     -0.028    2.908
    7321     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 HG2    -0.041    2.801
    7322     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 3HD1   -0.049    2.929
    7323     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 HG     -0.068    2.948
    7324     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 OG     -0.074    3.454
    7325     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A TYR 68 CE2    -0.090    3.550
    7326     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 CG     -0.104    3.564
    7327     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 CD     -0.117    3.577
    7328     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 HG     -0.124    2.734
    7329     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CS1.pdbqt #1/A LYS 54 HZ1    -0.129    3.009
    7330     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CS1.pdbqt #1/A SER 13 OG     -0.138    2.698
    7331     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A ALA 61 CB     -0.158    3.738
    7332     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 CG     -0.166    3.626
    7333     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LYS 10 CD     -0.172    3.632
    7334     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CS1.pdbqt #1/A LYS 54 HD3    -0.195    3.075
    7335     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLY 1 HN      -0.208    2.968
    7336     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A ALA 61 O      -0.211    3.571
    7337     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 CD1    -0.220    3.530
    7338     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 OE1    -0.227    3.467
    7339     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 HG2    -0.229    3.109
    7340     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A TYR 68 CD2    -0.237    3.697
    7341     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CS1.pdbqt #1/A ALA 61 HB3    -0.242    2.662
    7342     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLY 1 HA2     -0.267    3.147
    7343     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 CG     -0.272    3.732
    7344     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLU 58 OE1    -0.276    3.516
    7345     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 HA     -0.296    3.176
    7346     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 HD2    -0.304    3.064
    7347     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 2HD1   -0.327    2.937
    7348     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 CD     -0.330    3.790
    7349     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LYS 10 HB3    -0.331    3.091
    7350     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 CB     -0.332    3.912
    7351     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 CD1    -0.334    3.644
    7352     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A TYR 68 CZ     -0.337    3.797
    7353     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2CS1.pdbqt #1/A LYS 54 NZ     -0.359    3.864
    7354     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A SER 13 OG     -0.373    3.483
    7355     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LYS 10 HD2    -0.378    3.138
    7356     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A GLY 1 N       -0.379    3.764
    7357     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A PRO 11 CG     -0.380    3.840
    7358     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A TRP 46 HZ2    -0.386    3.146
    7359     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O   2CS1.pdbqt #1/A ALA 61 CB     -0.386    3.506
    7360     2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C   2CS1.pdbqt #1/A LEU 65 CD2    -0.388    3.968
    7361    
    7362 
    7363  
    7364 50 contacts 
    7365 
    7366 > hbonds :UNL showDist true radius 0.05 log true saveFile
    7367 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
    7368 > WRM-16.hbonds.txt
    7369    
    7370    
    7371     Finding intermodel H-bonds
    7372     Finding intramodel H-bonds
    7373     Constraints relaxed by 0.4 angstroms and 20 degrees
    7374     Models used:
    7375         1 2CS1.pdbqt
    7376         2.1 2CS1--WRM-16.result.pdbqt
    7377    
    7378     1 H-bonds
    7379     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7380     2CS1.pdbqt #1/A SER 13 OG  2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O  2CS1.pdbqt #1/A SER 13 HG  2.698  1.834
    7381    
    7382 
    7383  
    7384 1 hydrogen bonds found 
    7385 
    7386 > select :UNL
    7387 
    7388 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7389 
    7390 > label sel text "Ligand "
    7391 
    7392 > label height 1
    7393 
    7394 > ~select
    7395 
    7396 Nothing selected 
    7397 
    7398 > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
    7399 > ypos .95
    7400 
    7401 > 2dlabels text "2CS1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    7402 
    7403 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
    7404 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    7405 > true
    7406 
    7407 > select :UNL
    7408 
    7409 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7410 
    7411 > view sel
    7412 
    7413 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
    7414 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    7415 > true
    7416 
    7417 > close
    7418 
    7419 > wait 5
    7420 
    7421 > set bgColor white
    7422 
    7423 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2GU8.pdbqt
    7424 
    7425 Chain information for 2GU8.pdbqt #1 
    7426 --- 
    7427 Chain | Description 
    7428 A | No description available 
    7429 C | No description available 
    7430  
    7431 Opened 2GU8.pdbqt containing 1 structures (5803 atoms, 5874 bonds) 
    7432 
    7433 > wait 5
    7434 
    7435 > hide surfaces
    7436 
    7437 > hide atoms
    7438 
    7439 > show cartoons
    7440 
    7441 > wait 5
    7442 
    7443 > addh
    7444 
    7445 Summary of feedback from adding hydrogens to 2GU8.pdbqt #1 
    7446 --- 
    7447 warnings | Not adding hydrogens to /A VAL 15 CB because it is missing heavy-
    7448 atom bond partners 
    7449 Not adding hydrogens to /A LYS 16 CB because it is missing heavy-atom bond
    7450 partners 
    7451 Not adding hydrogens to /A GLU 17 CB because it is missing heavy-atom bond
    7452 partners 
    7453 Not adding hydrogens to /A LYS 21 CB because it is missing heavy-atom bond
    7454 partners 
    7455 notes | No usable SEQRES records for 2GU8.pdbqt (#1) chain A; guessing termini
    7456 instead 
    7457 No usable SEQRES records for 2GU8.pdbqt (#1) chain C; guessing termini instead 
    7458 Chain-initial residues that are actual N termini: /A SER 14, /C THR 505 
    7459 Chain-initial residues that are not actual N termini: /A LEU 198, /A ILE 339 
    7460 Chain-final residues that are actual C termini: /A PHE 350, /C ASP 524 
    7461 Chain-final residues that are not actual C termini: /A TRP 196, /A VAL 337 
    7462 290 hydrogen bonds 
    7463 Adding 'H' to /A LEU 198 
    7464 Adding 'H' to /A ILE 339 
    7465 /A TRP 196 is not terminus, removing H atom from 'C' 
    7466 /A VAL 337 is not terminus, removing H atom from 'C' 
    7467 -2 hydrogens added 
    7468  
    7469 
    7470 > wait 5
    7471 
    7472 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--
    7473 > WRM-16.result.pdbqt
    7474 
    7475 Summary of feedback from opening
    7476 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--WRM-16.result.pdbqt 
    7477 --- 
    7478 warnings | Ignored bad PDB record found on line 2 
    7479 REMARK VINA RESULT: -8.1 0.000 0.000 
    7480  
    7481 Ignored bad PDB record found on line 3 
    7482 REMARK 5 active torsions: 
    7483  
    7484 Ignored bad PDB record found on line 4 
    7485 REMARK status: ('A' for Active; 'I' for Inactive) 
    7486  
    7487 Ignored bad PDB record found on line 5 
    7488 REMARK 1 A between atoms: C_9 and O_15 
    7489  
    7490 Ignored bad PDB record found on line 6 
    7491 REMARK 2 A between atoms: C_10 and O_17 
    7492  
    7493 184 messages similar to the above omitted 
    7494  
    7495 Opened 2GU8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    7496 bonds) 
    7497 
    7498 > wait 5
    7499 
    7500 > close #2.2-9
    7501 
    7502 > wait 5
    7503 
    7504 > contacts :UNL radius 0.05 log true saveFile
    7505 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
    7506 > WRM-16.contacts.txt
    7507    
    7508    
    7509     Allowed overlap: -0.4
    7510     H-bond overlap reduction: 0.4
    7511     Ignore contacts between atoms separated by 4 bonds or less
    7512     Detect intra-residue contacts: False
    7513     Detect intra-molecule contacts: True
    7514    
    7515     57 contacts
    7516                       atom1                               atom2              overlap  distance
    7517     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 HG2    0.382    2.498
    7518     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 141 O      0.347    3.013
    7519     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ASP 301 HN     0.332    2.428
    7520     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 313 HD1    0.278    2.602
    7521     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 300 HA     0.244    2.516
    7522     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2GU8.pdbqt #1/A VAL 310 3HG2   0.217    2.663
    7523     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A VAL 310 CG2    0.191    3.269
    7524     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 HB2    0.173    2.707
    7525     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 HE     0.160    1.900
    7526     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 HE     0.104    2.506
    7527     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A VAL 310 1HG2   0.094    2.666
    7528     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 313 CD     0.077    3.503
    7529     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2GU8.pdbqt #1/A ASP 301 HB2    0.074    2.806
    7530     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ASP 301 HN     0.042    2.718
    7531     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A THR 299 HG1    0.035    1.985
    7532     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 CG     0.002    3.578
    7533     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 299 O      -0.001    3.241
    7534     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ASP 301 N      -0.038    3.423
    7535     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 300 HA     -0.045    2.655
    7536     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 CB     -0.051    3.631
    7537     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 1HH2   -0.078    2.098
    7538     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A PRO 141 HA     -0.089    2.549
    7539     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2GU8.pdbqt #1/A VAL 310 CG2    -0.106    3.686
    7540     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2GU8.pdbqt #1/A ASP 301 CB     -0.132    3.712
    7541     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 300 CA     -0.133    3.593
    7542     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 300 3HG2   -0.136    2.896
    7543     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 1HH2   -0.140    2.750
    7544     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 NE     -0.171    2.856
    7545     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A VAL 310 3HG2   -0.210    2.970
    7546     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A GLU 311 O      -0.241    3.601
    7547     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 313 CG     -0.249    3.829
    7548     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 CD1    -0.251    3.831
    7549     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 CD     -0.252    3.372
    7550     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 141 C      -0.252    3.832
    7551     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 299 O      -0.253    3.493
    7552     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 NE     -0.260    3.495
    7553     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ASP 301 N      -0.268    3.653
    7554     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 299 HB     -0.289    3.169
    7555     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 HG2    -0.290    3.170
    7556     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 CG     -0.293    3.873
    7557     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A PRO 141 CA     -0.296    3.456
    7558     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A VAL 310 CG1    -0.301    3.461
    7559     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ARG 144 HE     -0.306    3.186
    7560     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 300 CG2    -0.311    3.771
    7561     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A THR 300 CA     -0.313    3.433
    7562     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ASP 301 HB2    -0.319    3.079
    7563     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 N      -0.333    3.838
    7564     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 141 CA     -0.337    3.917
    7565     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PHE 145 CA     -0.342    3.922
    7566     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A ILE 305 1HD1   -0.361    3.121
    7567     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A THR 299 C      -0.363    3.483
    7568     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 141 HB2    -0.372    2.982
    7569     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 NH2    -0.373    3.018
    7570     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A THR 299 OG1    -0.378    2.898
    7571     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A THR 299 OG1    -0.384    3.494
    7572     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O   2GU8.pdbqt #1/A ARG 144 HG2    -0.393    2.813
    7573     2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C   2GU8.pdbqt #1/A PRO 141 HA     -0.395    3.275
    7574    
    7575 
    7576  
    7577 57 contacts 
    7578 
    7579 > hbonds :UNL showDist true radius 0.05 log true saveFile
    7580 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
    7581 > WRM-16.hbonds.txt
    7582    
    7583    
    7584     Finding intermodel H-bonds
    7585     Finding intramodel H-bonds
    7586     Constraints relaxed by 0.4 angstroms and 20 degrees
    7587     Models used:
    7588         1 2GU8.pdbqt
    7589         2.1 2GU8--WRM-16.result.pdbqt
    7590    
    7591     3 H-bonds
    7592     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7593     2GU8.pdbqt #1/A ARG 144 NE   2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O  2GU8.pdbqt #1/A ARG 144 HE    2.856  1.900
    7594     2GU8.pdbqt #1/A ARG 144 NH2  2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O  2GU8.pdbqt #1/A ARG 144 1HH2  3.018  2.098
    7595     2GU8.pdbqt #1/A THR 299 OG1  2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O  2GU8.pdbqt #1/A THR 299 HG1   2.898  1.985
    7596    
    7597 
    7598  
    7599 3 hydrogen bonds found 
    7600 
    7601 > select :UNL
    7602 
    7603 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7604 
    7605 > label sel text "Ligand "
    7606 
    7607 > label height 1
    7608 
    7609 > ~select
    7610 
    7611 Nothing selected 
    7612 
    7613 > 2dlabels text "Binding Energy: -8.1 kcal/mol" color red size 18 xpos .03
    7614 > ypos .95
    7615 
    7616 > 2dlabels text "2GU8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    7617 
    7618 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
    7619 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    7620 > true
    7621 
    7622 > select :UNL
    7623 
    7624 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7625 
    7626 > view sel
    7627 
    7628 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
    7629 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    7630 > true
    7631 
    7632 > close
    7633 
    7634 > wait 5
    7635 
    7636 > set bgColor white
    7637 
    7638 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VTB.pdbqt
    7639 
    7640 Chain information for 5VTB.pdbqt #1 
    7641 --- 
    7642 Chain | Description 
    7643 A | No description available 
    7644 B | No description available 
    7645  
    7646 Opened 5VTB.pdbqt containing 1 structures (5433 atoms, 5510 bonds) 
    7647 
    7648 > wait 5
    7649 
    7650 > hide surfaces
    7651 
    7652 > hide atoms
    7653 
    7654 > show cartoons
    7655 
    7656 > wait 5
    7657 
    7658 > addh
    7659 
    7660 Summary of feedback from adding hydrogens to 5VTB.pdbqt #1 
    7661 --- 
    7662 warnings | Not adding hydrogens to /A LYS 25 CB because it is missing heavy-
    7663 atom bond partners 
    7664 Not adding hydrogens to /A LYS 26 CB because it is missing heavy-atom bond
    7665 partners 
    7666 Not adding hydrogens to /A VAL 35 CB because it is missing heavy-atom bond
    7667 partners 
    7668 Not adding hydrogens to /A ASP 52 CB because it is missing heavy-atom bond
    7669 partners 
    7670 Not adding hydrogens to /A LYS 59 CB because it is missing heavy-atom bond
    7671 partners 
    7672 32 messages similar to the above omitted 
    7673 notes | No usable SEQRES records for 5VTB.pdbqt (#1) chain A; guessing termini
    7674 instead 
    7675 No usable SEQRES records for 5VTB.pdbqt (#1) chain B; guessing termini instead 
    7676 Chain-initial residues that are actual N termini: /A LYS 25, /B ARG 3 
    7677 Chain-initial residues that are not actual N termini: /A LYS 59, /A GLY 113,
    7678 /A PRO 363 
    7679 Chain-final residues that are actual C termini: /A ASP 411, /B GLU 16 
    7680 Chain-final residues that are not actual C termini: /A THR 54, /A ASN 88, /A
    7681 GLU 352 
    7682 287 hydrogen bonds 
    7683 Adding 'H' to /A LYS 59 
    7684 Adding 'H' to /A GLY 113 
    7685 /A THR 54 is not terminus, removing H atom from 'C' 
    7686 /A ASN 88 is not terminus, removing H atom from 'C' 
    7687 /A GLU 352 is not terminus, removing H atom from 'C' 
    7688 -2 hydrogens added 
    7689  
    7690 
    7691 > wait 5
    7692 
    7693 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--
    7694 > WRM-16.result.pdbqt
    7695 
    7696 Summary of feedback from opening
    7697 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--WRM-16.result.pdbqt 
    7698 --- 
    7699 warnings | Ignored bad PDB record found on line 2 
    7700 REMARK VINA RESULT: -8.4 0.000 0.000 
    7701  
    7702 Ignored bad PDB record found on line 3 
    7703 REMARK 5 active torsions: 
    7704  
    7705 Ignored bad PDB record found on line 4 
    7706 REMARK status: ('A' for Active; 'I' for Inactive) 
    7707  
    7708 Ignored bad PDB record found on line 5 
    7709 REMARK 1 A between atoms: C_9 and O_15 
    7710  
    7711 Ignored bad PDB record found on line 6 
    7712 REMARK 2 A between atoms: C_10 and O_17 
    7713  
    7714 184 messages similar to the above omitted 
    7715  
    7716 Opened 5VTB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    7717 bonds) 
    7718 
    7719 > wait 5
    7720 
    7721 > close #2.2-9
    7722 
    7723 > wait 5
    7724 
    7725 > contacts :UNL radius 0.05 log true saveFile
    7726 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
    7727 > WRM-16.contacts.txt
    7728    
    7729    
    7730     Allowed overlap: -0.4
    7731     H-bond overlap reduction: 0.4
    7732     Ignore contacts between atoms separated by 4 bonds or less
    7733     Detect intra-residue contacts: False
    7734     Detect intra-molecule contacts: True
    7735    
    7736     47 contacts
    7737                       atom1                               atom2              overlap  distance
    7738     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 324 2HE2   0.542    2.338
    7739     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 HB2    0.411    2.469
    7740     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 324 NE2    0.359    3.146
    7741     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A TRP 382 O      0.261    3.099
    7742     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A TRP 185 HN     0.260    2.500
    7743     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 CB     0.243    3.337
    7744     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A PRO 327 HB2    0.217    2.543
    7745     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 327 HG1    0.111    2.769
    7746     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 184 HA     0.106    2.654
    7747     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A PRO 327 HB2    0.056    2.554
    7748     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 234 HG     -0.008    2.028
    7749     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 CA     -0.067    3.647
    7750     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 280 HA     -0.085    2.505
    7751     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 327 CG     -0.089    3.669
    7752     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A TRP 325 HB1    -0.103    2.523
    7753     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 48 2HE2    -0.108    2.988
    7754     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A TRP 185 N      -0.114    3.499
    7755     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 324 2HE2   -0.124    2.734
    7756     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 184 OG     -0.150    3.410
    7757     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 234 HG     -0.157    2.767
    7758     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 327 HB2    -0.165    3.045
    7759     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 327 CB     -0.167    3.747
    7760     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A TRP 382 HB2    -0.167    2.927
    7761     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 184 CA     -0.177    3.637
    7762     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 184 HA     -0.183    2.943
    7763     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A PRO 327 CB     -0.192    3.652
    7764     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A PRO 327 CB     -0.197    3.507
    7765     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A LEU 183 O      -0.205    3.565
    7766     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 N      -0.232    3.737
    7767     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 234 OG     -0.239    2.759
    7768     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 CD     -0.256    3.836
    7769     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A TRP 325 O      -0.266    3.506
    7770     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 48 1HE2    -0.291    3.051
    7771     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A TRP 185 HN     -0.309    3.069
    7772     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A GLN 324 OE1    -0.311    3.251
    7773     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A VAL 233 O      -0.314    3.674
    7774     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 324 CD     -0.319    3.899
    7775     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A SER 234 OG     -0.319    3.429
    7776     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 234 OG     -0.328    2.888
    7777     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 48 NE2     -0.330    3.715
    7778     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 HA     -0.334    3.214
    7779     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 234 CB     -0.341    3.461
    7780     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 324 NE2    -0.343    3.728
    7781     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A SER 234 CB     -0.350    3.510
    7782     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O   5VTB.pdbqt #1/A LEU 279 O      -0.370    3.270
    7783     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C   5VTB.pdbqt #1/A GLN 48 1HE2    -0.379    3.139
    7784     5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL  5VTB.pdbqt #1/A PRO 384 CG     -0.388    3.968
    7785    
    7786 
    7787  
    7788 47 contacts 
    7789 
    7790 > hbonds :UNL showDist true radius 0.05 log true saveFile
    7791 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
    7792 > WRM-16.hbonds.txt
    7793    
    7794    
    7795     Finding intermodel H-bonds
    7796     Finding intramodel H-bonds
    7797     Constraints relaxed by 0.4 angstroms and 20 degrees
    7798     Models used:
    7799         1 5VTB.pdbqt
    7800         2.1 5VTB--WRM-16.result.pdbqt
    7801    
    7802     1 H-bonds
    7803     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7804     5VTB.pdbqt #1/A SER 234 OG  5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O  5VTB.pdbqt #1/A SER 234 HG  2.759  2.028
    7805    
    7806 
    7807  
    7808 1 hydrogen bonds found 
    7809 
    7810 > select :UNL
    7811 
    7812 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7813 
    7814 > label sel text "Ligand "
    7815 
    7816 > label height 1
    7817 
    7818 > ~select
    7819 
    7820 Nothing selected 
    7821 
    7822 > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
    7823 > ypos .95
    7824 
    7825 > 2dlabels text "5VTB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    7826 
    7827 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
    7828 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    7829 > true
    7830 
    7831 > select :UNL
    7832 
    7833 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7834 
    7835 > view sel
    7836 
    7837 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
    7838 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    7839 > true
    7840 
    7841 > close
    7842 
    7843 > wait 5
    7844 
    7845 > set bgColor white
    7846 
    7847 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D3J.pdbqt
    7848 
    7849 Chain information for 2D3J.pdbqt #1 
    7850 --- 
    7851 Chain | Description 
    7852 A | No description available 
    7853  
    7854 Opened 2D3J.pdbqt containing 1 structures (2441 atoms, 2470 bonds) 
    7855 
    7856 > wait 5
    7857 
    7858 > hide surfaces
    7859 
    7860 > hide atoms
    7861 
    7862 > show cartoons
    7863 
    7864 > wait 5
    7865 
    7866 > addh
    7867 
    7868 Summary of feedback from adding hydrogens to 2D3J.pdbqt #1 
    7869 --- 
    7870 notes | No usable SEQRES records for 2D3J.pdbqt (#1) chain A; guessing termini
    7871 instead 
    7872 Chain-initial residues that are actual N termini: /A GLY 1 
    7873 Chain-initial residues that are not actual N termini: 
    7874 Chain-final residues that are actual C termini: /A GLU 157 
    7875 Chain-final residues that are not actual C termini: 
    7876 134 hydrogen bonds 
    7877 2 hydrogens added 
    7878  
    7879 
    7880 > wait 5
    7881 
    7882 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--
    7883 > WRM-16.result.pdbqt
    7884 
    7885 Summary of feedback from opening
    7886 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--WRM-16.result.pdbqt 
    7887 --- 
    7888 warnings | Ignored bad PDB record found on line 2 
    7889 REMARK VINA RESULT: -6.9 0.000 0.000 
    7890  
    7891 Ignored bad PDB record found on line 3 
    7892 REMARK 5 active torsions: 
    7893  
    7894 Ignored bad PDB record found on line 4 
    7895 REMARK status: ('A' for Active; 'I' for Inactive) 
    7896  
    7897 Ignored bad PDB record found on line 5 
    7898 REMARK 1 A between atoms: C_9 and O_15 
    7899  
    7900 Ignored bad PDB record found on line 6 
    7901 REMARK 2 A between atoms: C_10 and O_17 
    7902  
    7903 184 messages similar to the above omitted 
    7904  
    7905 Opened 2D3J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    7906 bonds) 
    7907 
    7908 > wait 5
    7909 
    7910 > close #2.2-9
    7911 
    7912 > wait 5
    7913 
    7914 > contacts :UNL radius 0.05 log true saveFile
    7915 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
    7916 > WRM-16.contacts.txt
    7917    
    7918    
    7919     Allowed overlap: -0.4
    7920     H-bond overlap reduction: 0.4
    7921     Ignore contacts between atoms separated by 4 bonds or less
    7922     Detect intra-residue contacts: False
    7923     Detect intra-molecule contacts: True
    7924    
    7925     45 contacts
    7926                       atom1                               atom2              overlap  distance
    7927     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2D3J.pdbqt #1/A LEU 85 2HD1    0.384    2.496
    7928     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 55 HB3     0.246    2.514
    7929     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HZ     0.218    2.542
    7930     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2D3J.pdbqt #1/A LEU 85 CD1     0.198    3.382
    7931     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A VAL 123 3HG1   0.151    2.609
    7932     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 49 N       0.137    3.368
    7933     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CZ     0.129    3.451
    7934     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ILE 148 3HD1   0.115    2.645
    7935     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ILE 148 3HG2   0.068    2.692
    7936     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 49 HB3     0.051    2.829
    7937     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 HD3     -0.008    2.888
    7938     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 55 CB      -0.044    3.504
    7939     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 HD3     -0.047    2.657
    7940     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 HD3     -0.064    2.824
    7941     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 49 CA      -0.071    3.651
    7942     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CD2    -0.087    3.667
    7943     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HZ     -0.097    2.977
    7944     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ALA 49 CB      -0.100    3.680
    7945     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CE2    -0.125    3.705
    7946     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 CD      -0.137    3.717
    7947     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HZ     -0.142    2.752
    7948     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CZ     -0.164    3.624
    7949     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ILE 148 CD1    -0.196    3.656
    7950     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CB     -0.221    3.681
    7951     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A VAL 123 CG1    -0.221    3.681
    7952     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A VAL 123 3HG1   -0.232    2.992
    7953     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CG     -0.235    3.695
    7954     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PRO 54 HB2     -0.236    2.996
    7955     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CD2    -0.247    3.557
    7956     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A LYS 48 C       -0.250    3.830
    7957     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ILE 148 3HG2   -0.280    3.040
    7958     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ILE 148 CG2    -0.287    3.747
    7959     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HD2    -0.289    3.169
    7960     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CD1    -0.292    3.752
    7961     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CE1    -0.296    3.876
    7962     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D3J.pdbqt #1/A ARG 47 NH1     -0.304    2.949
    7963     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HZ     -0.325    3.085
    7964     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O   2D3J.pdbqt #1/A ARG 47 1HH1    -0.329    2.349
    7965     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 CD      -0.348    3.658
    7966     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CG     -0.349    3.659
    7967     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 CB     -0.352    3.812
    7968     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HE2    -0.357    3.237
    7969     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 CD      -0.365    3.825
    7970     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A ARG 47 O       -0.370    3.730
    7971     2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C   2D3J.pdbqt #1/A PHE 150 HB3    -0.374    3.134
    7972    
    7973 
    7974  
    7975 45 contacts 
    7976 
    7977 > hbonds :UNL showDist true radius 0.05 log true saveFile
    7978 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
    7979 > WRM-16.hbonds.txt
    7980    
    7981    
    7982     Finding intermodel H-bonds
    7983     Finding intramodel H-bonds
    7984     Constraints relaxed by 0.4 angstroms and 20 degrees
    7985     Models used:
    7986         1 2D3J.pdbqt
    7987         2.1 2D3J--WRM-16.result.pdbqt
    7988    
    7989     0 H-bonds
    7990     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7991    
    7992 
    7993  
    7994 0 hydrogen bonds found 
    7995 
    7996 > select :UNL
    7997 
    7998 28 atoms, 31 bonds, 1 residue, 1 model selected 
    7999 
    8000 > label sel text "Ligand "
    8001 
    8002 > label height 1
    8003 
    8004 > ~select
    8005 
    8006 Nothing selected 
    8007 
    8008 > 2dlabels text "Binding Energy: -6.9 kcal/mol" color red size 18 xpos .03
    8009 > ypos .95
    8010 
    8011 > 2dlabels text "2D3J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    8012 
    8013 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
    8014 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    8015 > true
    8016 
    8017 > select :UNL
    8018 
    8019 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8020 
    8021 > view sel
    8022 
    8023 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
    8024 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    8025 > true
    8026 
    8027 > close
    8028 
    8029 > wait 5
    8030 
    8031 > set bgColor white
    8032 
    8033 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2E50.pdbqt
    8034 
    8035 Chain information for 2E50.pdbqt #1 
    8036 --- 
    8037 Chain | Description 
    8038 A | No description available 
    8039 B | No description available 
    8040 P | No description available 
    8041 Q | No description available 
    8042  
    8043 Opened 2E50.pdbqt containing 1 structures (11470 atoms, 11602 bonds) 
    8044 
    8045 > wait 5
    8046 
    8047 > hide surfaces
    8048 
    8049 > hide atoms
    8050 
    8051 > show cartoons
    8052 
    8053 > wait 5
    8054 
    8055 > addh
    8056 
    8057 Summary of feedback from adding hydrogens to 2E50.pdbqt #1 
    8058 --- 
    8059 warning | Not adding hydrogens to /B MET 145 CB because it is missing heavy-
    8060 atom bond partners 
    8061 notes | No usable SEQRES records for 2E50.pdbqt (#1) chain A; guessing termini
    8062 instead 
    8063 No usable SEQRES records for 2E50.pdbqt (#1) chain B; guessing termini instead 
    8064 No usable SEQRES records for 2E50.pdbqt (#1) chain P; guessing termini instead 
    8065 No usable SEQRES records for 2E50.pdbqt (#1) chain Q; guessing termini instead 
    8066 Chain-initial residues that are actual N termini: /A MET 1, /B SER 24, /P MET
    8067 1, /Q SER 24 
    8068 Chain-initial residues that are not actual N termini: /A ASP 21, /A SER 152,
    8069 /A PHE 189, /A ALA 201, /B SER 152, /B PHE 189, /B GLY 200, /P ALA 20, /P SER
    8070 152, /P PHE 189, /P GLY 200, /Q SER 152, /Q PHE 189, /Q ALA 201 
    8071 Chain-final residues that are actual C termini: /A VAL 222, /B PRO 223, /P VAL
    8072 222, /Q PRO 223 
    8073 Chain-final residues that are not actual C termini: /A SER 15, /A HIS 144, /A
    8074 MET 166, /A THR 194, /B MET 145, /B MET 166, /B THR 194, /P ASN 16, /P HIS
    8075 144, /P THR 167, /P THR 194, /Q HIS 144, /Q TRP 160, /Q THR 194 
    8076 568 hydrogen bonds 
    8077 Adding 'H' to /A ASP 21 
    8078 Adding 'H' to /A SER 152 
    8079 Adding 'H' to /A PHE 189 
    8080 Adding 'H' to /A ALA 201 
    8081 Adding 'H' to /B SER 152 
    8082 9 messages similar to the above omitted 
    8083 /A SER 15 is not terminus, removing H atom from 'C' 
    8084 /A HIS 144 is not terminus, removing H atom from 'C' 
    8085 /A MET 166 is not terminus, removing H atom from 'C' 
    8086 /A THR 194 is not terminus, removing H atom from 'C' 
    8087 /B MET 145 is not terminus, removing H atom from 'C' 
    8088 9 messages similar to the above omitted 
    8089 -41 hydrogens added 
    8090  
    8091 
    8092 > wait 5
    8093 
    8094 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--
    8095 > WRM-16.result.pdbqt
    8096 
    8097 Summary of feedback from opening
    8098 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--WRM-16.result.pdbqt 
    8099 --- 
    8100 warnings | Ignored bad PDB record found on line 2 
    8101 REMARK VINA RESULT: -8.8 0.000 0.000 
    8102  
    8103 Ignored bad PDB record found on line 3 
    8104 REMARK 5 active torsions: 
    8105  
    8106 Ignored bad PDB record found on line 4 
    8107 REMARK status: ('A' for Active; 'I' for Inactive) 
    8108  
    8109 Ignored bad PDB record found on line 5 
    8110 REMARK 1 A between atoms: C_9 and O_15 
    8111  
    8112 Ignored bad PDB record found on line 6 
    8113 REMARK 2 A between atoms: C_10 and O_17 
    8114  
    8115 184 messages similar to the above omitted 
    8116  
    8117 Opened 2E50--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    8118 bonds) 
    8119 
    8120 > wait 5
    8121 
    8122 > close #2.2-9
    8123 
    8124 > wait 5
    8125 
    8126 > contacts :UNL radius 0.05 log true saveFile
    8127 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
    8128 > WRM-16.contacts.txt
    8129    
    8130    
    8131     Allowed overlap: -0.4
    8132     H-bond overlap reduction: 0.4
    8133     Ignore contacts between atoms separated by 4 bonds or less
    8134     Detect intra-residue contacts: False
    8135     Detect intra-molecule contacts: True
    8136    
    8137     49 contacts
    8138                       atom1                               atom2             overlap  distance
    8139     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 HB2   0.217    2.543
    8140     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2E50.pdbqt #1/A PRO 214 HG1   0.160    2.720
    8141     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 HN    0.145    2.735
    8142     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O   2E50.pdbqt #1/A GLN 65 HB2    0.121    2.339
    8143     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 HB1   0.092    2.668
    8144     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A TRP 213 HD1   0.078    2.682
    8145     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 O      0.052    3.308
    8146     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A TRP 213 CD1   -0.046    3.506
    8147     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2E50.pdbqt #1/A PRO 214 CG    -0.080    3.660
    8148     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASP 117 HN    -0.136    2.896
    8149     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 HB1    -0.144    3.024
    8150     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O   2E50.pdbqt #1/A GLN 65 CB     -0.152    3.312
    8151     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 N     -0.156    3.541
    8152     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 CB    -0.162    3.622
    8153     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 HB2   -0.168    2.928
    8154     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CE1    -0.182    3.642
    8155     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 CB     -0.188    3.768
    8156     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 N     -0.196    3.701
    8157     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 HB1    -0.198    2.808
    8158     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A TRP 213 HE1   -0.224    2.984
    8159     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 HB1    -0.225    2.835
    8160     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 HB1   -0.236    3.116
    8161     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CZ     -0.245    3.705
    8162     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 CB    -0.258    3.718
    8163     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CZ     -0.261    3.721
    8164     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 NE     -0.263    3.648
    8165     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 CZ     -0.277    3.737
    8166     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CE2    -0.278    3.738
    8167     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 NH1    -0.279    3.664
    8168     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O   2E50.pdbqt #1/A ASN 61 O      -0.292    3.232
    8169     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 HD2    -0.294    3.054
    8170     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 HN    -0.296    3.056
    8171     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 O     -0.298    3.538
    8172     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 HD2    -0.303    3.063
    8173     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 OD1    -0.315    3.405
    8174     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 N     -0.318    3.703
    8175     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 114 CB    -0.319    3.899
    8176     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ARG 64 CD     -0.323    3.783
    8177     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL  2E50.pdbqt #1/A PRO 214 CB    -0.323    3.903
    8178     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 ND2    -0.330    3.835
    8179     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 OD1    -0.332    3.422
    8180     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CE2    -0.337    3.797
    8181     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CZ     -0.340    3.650
    8182     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A ASN 61 CA     -0.362    3.942
    8183     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A TRP 213 NE1   -0.364    3.749
    8184     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CZ     -0.365    3.825
    8185     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A PHE 68 CZ     -0.379    3.839
    8186     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A GLU 116 CB    -0.383    3.843
    8187     2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C   2E50.pdbqt #1/A TRP 213 NE1   -0.385    3.770
    8188    
    8189 
    8190  
    8191 49 contacts 
    8192 
    8193 > hbonds :UNL showDist true radius 0.05 log true saveFile
    8194 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
    8195 > WRM-16.hbonds.txt
    8196    
    8197    
    8198     Finding intermodel H-bonds
    8199     Finding intramodel H-bonds
    8200     Constraints relaxed by 0.4 angstroms and 20 degrees
    8201     Models used:
    8202         1 2E50.pdbqt
    8203         2.1 2E50--WRM-16.result.pdbqt
    8204    
    8205     0 H-bonds
    8206     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8207    
    8208 
    8209  
    8210 0 hydrogen bonds found 
    8211 
    8212 > select :UNL
    8213 
    8214 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8215 
    8216 > label sel text "Ligand "
    8217 
    8218 > label height 1
    8219 
    8220 > ~select
    8221 
    8222 Nothing selected 
    8223 
    8224 > 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
    8225 > ypos .95
    8226 
    8227 > 2dlabels text "2E50 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    8228 
    8229 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
    8230 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    8231 > true
    8232 
    8233 > select :UNL
    8234 
    8235 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8236 
    8237 > view sel
    8238 
    8239 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
    8240 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    8241 > true
    8242 
    8243 > close
    8244 
    8245 > wait 5
    8246 
    8247 > set bgColor white
    8248 
    8249 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VBN.pdbqt
    8250 
    8251 Chain information for 5VBN.pdbqt #1 
    8252 --- 
    8253 Chain | Description 
    8254 A E | No description available 
    8255 B F | No description available 
    8256  
    8257 Opened 5VBN.pdbqt containing 1 structures (17529 atoms, 17769 bonds) 
    8258 
    8259 > wait 5
    8260 
    8261 > hide surfaces
    8262 
    8263 > hide atoms
    8264 
    8265 > show cartoons
    8266 
    8267 > wait 5
    8268 
    8269 > addh
    8270 
    8271 Summary of feedback from adding hydrogens to 5VBN.pdbqt #1 
    8272 --- 
    8273 notes | No usable SEQRES records for 5VBN.pdbqt (#1) chain A; guessing termini
    8274 instead 
    8275 No usable SEQRES records for 5VBN.pdbqt (#1) chain B; guessing termini instead 
    8276 No usable SEQRES records for 5VBN.pdbqt (#1) chain E; guessing termini instead 
    8277 No usable SEQRES records for 5VBN.pdbqt (#1) chain F; guessing termini instead 
    8278 Chain-initial residues that are actual N termini: /A HIS 84, /B SER 2150, /E
    8279 HIS 84, /F SER 2150 
    8280 Chain-initial residues that are not actual N termini: /A PHE 163, /B PRO 2183,
    8281 /E PHE 163, /F PRO 2183 
    8282 Chain-final residues that are actual C termini: /A PHE 527, /B PRO 2282, /E
    8283 PHE 527, /F PRO 2282 
    8284 Chain-final residues that are not actual C termini: /A GLU 145, /B SER 2174,
    8285 /E GLU 145, /F SER 2174 
    8286 854 hydrogen bonds 
    8287 Adding 'H' to /A PHE 163 
    8288 Adding 'H' to /E PHE 163 
    8289 /A GLU 145 is not terminus, removing H atom from 'C' 
    8290 /B SER 2174 is not terminus, removing H atom from 'C' 
    8291 /E GLU 145 is not terminus, removing H atom from 'C' 
    8292 /F SER 2174 is not terminus, removing H atom from 'C' 
    8293 35 hydrogens added 
    8294  
    8295 
    8296 > wait 5
    8297 
    8298 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--
    8299 > WRM-16.result.pdbqt
    8300 
    8301 Summary of feedback from opening
    8302 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--WRM-16.result.pdbqt 
    8303 --- 
    8304 warnings | Ignored bad PDB record found on line 2 
    8305 REMARK VINA RESULT: -8.3 0.000 0.000 
    8306  
    8307 Ignored bad PDB record found on line 3 
    8308 REMARK 5 active torsions: 
    8309  
    8310 Ignored bad PDB record found on line 4 
    8311 REMARK status: ('A' for Active; 'I' for Inactive) 
    8312  
    8313 Ignored bad PDB record found on line 5 
    8314 REMARK 1 A between atoms: C_9 and O_15 
    8315  
    8316 Ignored bad PDB record found on line 6 
    8317 REMARK 2 A between atoms: C_10 and O_17 
    8318  
    8319 184 messages similar to the above omitted 
    8320  
    8321 Opened 5VBN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    8322 bonds) 
    8323 
    8324 > wait 5
    8325 
    8326 > close #2.2-9
    8327 
    8328 > wait 5
    8329 
    8330 > contacts :UNL radius 0.05 log true saveFile
    8331 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
    8332 > WRM-16.contacts.txt
    8333    
    8334    
    8335     Allowed overlap: -0.4
    8336     H-bond overlap reduction: 0.4
    8337     Ignore contacts between atoms separated by 4 bonds or less
    8338     Detect intra-residue contacts: False
    8339     Detect intra-molecule contacts: True
    8340    
    8341     63 contacts
    8342                      atom1                                atom2              overlap  distance
    8343     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LEU 190 1HD2    0.442    2.438
    8344     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B LEU 2216 HB2    0.235    2.525
    8345     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LEU 190 CD2     0.213    3.367
    8346     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A GLN 189 O       0.052    3.308
    8347     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HG2     0.023    2.737
    8348     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB2     0.015    2.595
    8349     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HB1     -0.011    2.621
    8350     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B SER 2231 HG     -0.027    2.787
    8351     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A THR 188 3HG2    -0.054    2.814
    8352     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HB1     -0.055    2.815
    8353     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB2     -0.081    2.841
    8354     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HA      -0.095    2.855
    8355     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CB      -0.121    3.581
    8356     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB2     -0.126    2.886
    8357     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PHE 130 CZ      -0.136    3.596
    8358     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A ALA 221 HB1     -0.136    2.896
    8359     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB2     -0.139    3.019
    8360     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A ALA 221 HB1     -0.152    2.912
    8361     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CB      -0.156    3.616
    8362     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A MET 186 CE      -0.163    3.623
    8363     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HD1     -0.168    3.048
    8364     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B LEU 2216 CB     -0.173    3.633
    8365     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B SER 2231 OG     -0.175    3.555
    8366     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HA      -0.177    2.937
    8367     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A GLN 189 C       -0.183    3.763
    8368     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CA      -0.202    3.662
    8369     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CB      -0.204    3.664
    8370     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CG      -0.206    3.666
    8371     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HB1     -0.216    2.826
    8372     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A ALA 221 CB      -0.222    3.682
    8373     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B SER 2231 OG     -0.228    3.488
    8374     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LEU 190 HA      -0.229    3.109
    8375     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LEU 456 3HD1    -0.231    3.111
    8376     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PHE 130 CE2     -0.231    3.691
    8377     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A MET 186 HE2     -0.236    2.996
    8378     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O  5VBN.pdbqt #1/A GLU 220 OE2     -0.242    3.182
    8379     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B SER 2231 HG     -0.247    3.007
    8380     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B LEU 2216 3HD1   -0.254    3.014
    8381     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A THR 188 HB      -0.257    3.137
    8382     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PHE 130 CE2     -0.260    3.720
    8383     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CB      -0.262    3.722
    8384     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CB      -0.265    3.725
    8385     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CB      -0.268    3.578
    8386     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O  5VBN.pdbqt #1/B LEU 2216 O      -0.275    3.175
    8387     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LYS 126 HE2     -0.301    3.181
    8388     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB1     -0.303    3.063
    8389     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CA      -0.313    3.773
    8390     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CB      -0.313    3.773
    8391     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A ALA 221 CB      -0.323    3.783
    8392     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A MET 186 HE2     -0.328    3.088
    8393     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A THR 188 CG2     -0.330    3.790
    8394     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A GLU 220 OE2     -0.346    3.586
    8395     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B LEU 2216 O      -0.348    3.588
    8396     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CB      -0.353    3.663
    8397     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HG2     -0.363    3.123
    8398     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HE1     -0.366    2.976
    8399     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 HG2     -0.374    3.134
    8400     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A LYS 126 CE      -0.382    3.962
    8401     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CG      -0.383    3.843
    8402     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 HB1     -0.385    2.995
    8403     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A PRO 455 CG      -0.387    3.847
    8404     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/A TYR 457 CD1     -0.395    3.975
    8405     5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C  5VBN.pdbqt #1/B LEU 2216 HB2    -0.398    3.158
    8406    
    8407 
    8408  
    8409 63 contacts 
    8410 
    8411 > hbonds :UNL showDist true radius 0.05 log true saveFile
    8412 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
    8413 > WRM-16.hbonds.txt
    8414    
    8415    
    8416     Finding intermodel H-bonds
    8417     Finding intramodel H-bonds
    8418     Constraints relaxed by 0.4 angstroms and 20 degrees
    8419     Models used:
    8420         1 5VBN.pdbqt
    8421         2.1 5VBN--WRM-16.result.pdbqt
    8422    
    8423     0 H-bonds
    8424     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8425    
    8426 
    8427  
    8428 0 hydrogen bonds found 
    8429 
    8430 > select :UNL
    8431 
    8432 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8433 
    8434 > label sel text "Ligand "
    8435 
    8436 > label height 1
    8437 
    8438 > ~select
    8439 
    8440 Nothing selected 
    8441 
    8442 > 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
    8443 > ypos .95
    8444 
    8445 > 2dlabels text "5VBN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    8446 
    8447 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
    8448 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    8449 > true
    8450 
    8451 > select :UNL
    8452 
    8453 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8454 
    8455 > view sel
    8456 
    8457 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
    8458 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    8459 > true
    8460 
    8461 > close
    8462 
    8463 > wait 5
    8464 
    8465 > set bgColor white
    8466 
    8467 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3ALN.pdbqt
    8468 
    8469 Chain information for 3ALN.pdbqt #1 
    8470 --- 
    8471 Chain | Description 
    8472 A | No description available 
    8473 B | No description available 
    8474 C | No description available 
    8475  
    8476 Opened 3ALN.pdbqt containing 1 structures (11428 atoms, 11539 bonds) 
    8477 
    8478 > wait 5
    8479 
    8480 > hide surfaces
    8481 
    8482 > hide atoms
    8483 
    8484 > show cartoons
    8485 
    8486 > wait 5
    8487 
    8488 > addh
    8489 
    8490 Summary of feedback from adding hydrogens to 3ALN.pdbqt #1 
    8491 --- 
    8492 warnings | Not adding hydrogens to /A SER 83 CB because it is missing heavy-
    8493 atom bond partners 
    8494 Not adding hydrogens to /A LYS 86 CB because it is missing heavy-atom bond
    8495 partners 
    8496 Not adding hydrogens to /A LYS 88 CB because it is missing heavy-atom bond
    8497 partners 
    8498 Not adding hydrogens to /A LEU 105 C because it is missing heavy-atom bond
    8499 partners 
    8500 Not adding hydrogens to /A ASP 138 CB because it is missing heavy-atom bond
    8501 partners 
    8502 30 messages similar to the above omitted 
    8503 The following atoms were skipped as donors/acceptors due to missing heavy-atom
    8504 bond partners: /A PRO 308 N 
    8505 notes | No usable SEQRES records for 3ALN.pdbqt (#1) chain A; guessing termini
    8506 instead 
    8507 No usable SEQRES records for 3ALN.pdbqt (#1) chain B; guessing termini instead 
    8508 No usable SEQRES records for 3ALN.pdbqt (#1) chain C; guessing termini instead 
    8509 Chain-initial residues that are actual N termini: /A SER 83, /B SER 84, /C GLU
    8510 100 
    8511 Chain-initial residues that are not actual N termini: /A TYR 284, /A THR 318,
    8512 /B TYR 284, /B ASP 324, /C ASN 117, /C ILE 127, /C CYS 158, /C CYS 174, /C LYS
    8513 231, /C SER 288, /C PRO 325 
    8514 Chain-final residues that are actual C termini: /A PRO 389, /B ALA 390, /C ALA
    8515 390 
    8516 Chain-final residues that are not actual C termini: /A GLN 253, /A TRP 310, /B
    8517 LEU 254, /B PRO 308, /C GLU 107, /C VAL 120, /C THR 136, /C TYR 165, /C LYS
    8518 224, /C PHE 248, /C PHE 305 
    8519 465 hydrogen bonds 
    8520 Adding 'H' to /A TYR 284 
    8521 Adding 'H' to /A THR 318 
    8522 Adding 'H' to /B TYR 284 
    8523 Adding 'H' to /B ASP 324 
    8524 Adding 'H' to /C ASN 117 
    8525 5 messages similar to the above omitted 
    8526 /A GLN 253 is not terminus, removing H atom from 'C' 
    8527 /A TRP 310 is not terminus, removing H atom from 'C' 
    8528 /B LEU 254 is not terminus, removing H atom from 'C' 
    8529 /B PRO 308 is not terminus, removing H atom from 'C' 
    8530 /C GLU 107 is not terminus, removing H atom from 'C' 
    8531 6 messages similar to the above omitted 
    8532 -6 hydrogens added 
    8533  
    8534 
    8535 > wait 5
    8536 
    8537 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--
    8538 > WRM-16.result.pdbqt
    8539 
    8540 Summary of feedback from opening
    8541 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--WRM-16.result.pdbqt 
    8542 --- 
    8543 warnings | Ignored bad PDB record found on line 2 
    8544 REMARK VINA RESULT: -8.7 0.000 0.000 
    8545  
    8546 Ignored bad PDB record found on line 3 
    8547 REMARK 5 active torsions: 
    8548  
    8549 Ignored bad PDB record found on line 4 
    8550 REMARK status: ('A' for Active; 'I' for Inactive) 
    8551  
    8552 Ignored bad PDB record found on line 5 
    8553 REMARK 1 A between atoms: C_9 and O_15 
    8554  
    8555 Ignored bad PDB record found on line 6 
    8556 REMARK 2 A between atoms: C_10 and O_17 
    8557  
    8558 184 messages similar to the above omitted 
    8559  
    8560 Opened 3ALN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    8561 bonds) 
    8562 
    8563 > wait 5
    8564 
    8565 > close #2.2-9
    8566 
    8567 > wait 5
    8568 
    8569 > contacts :UNL radius 0.05 log true saveFile
    8570 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
    8571 > WRM-16.contacts.txt
    8572    
    8573    
    8574     Allowed overlap: -0.4
    8575     H-bond overlap reduction: 0.4
    8576     Ignore contacts between atoms separated by 4 bonds or less
    8577     Detect intra-residue contacts: False
    8578     Detect intra-molecule contacts: True
    8579    
    8580     50 contacts
    8581                       atom1                               atom2              overlap  distance
    8582     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A TYR 113 HN     0.426    2.454
    8583     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 HA1    0.385    2.375
    8584     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LYS 131 HE1    0.145    2.615
    8585     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A THR 183 HA     0.134    2.626
    8586     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 HA1    0.097    2.513
    8587     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A TYR 113 N      0.090    3.415
    8588     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A VAL 116 3HG2   0.087    2.523
    8589     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LYS 187 HE1    0.085    2.795
    8590     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A LYS 131 HZ1    0.045    2.835
    8591     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 1HG2   0.033    2.727
    8592     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 HA1    0.027    2.733
    8593     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A MET 181 O      -0.005    3.245
    8594     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 CA     -0.019    3.479
    8595     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LEU 236 3HD1   -0.024    2.904
    8596     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LYS 131 CE     -0.041    3.501
    8597     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A MET 178 SD     -0.068    3.730
    8598     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LEU 236 CD1    -0.070    3.650
    8599     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O   3ALN.pdbqt #1/A VAL 116 3HG2   -0.075    2.495
    8600     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A SER 233 HG     -0.104    2.864
    8601     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 1HG2   -0.125    2.885
    8602     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A ALA 112 N      -0.153    3.658
    8603     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LYS 187 CE     -0.159    3.739
    8604     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LYS 131 NZ     -0.161    3.546
    8605     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 CG2    -0.166    3.626
    8606     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A LYS 131 NZ     -0.194    3.699
    8607     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 HA1    -0.208    2.968
    8608     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A THR 183 CA     -0.221    3.681
    8609     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O   3ALN.pdbqt #1/A ALA 129 CB     -0.224    3.384
    8610     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 1HG2   -0.224    2.984
    8611     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 CG2    -0.237    3.697
    8612     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O   3ALN.pdbqt #1/A ALA 129 HB2    -0.237    2.697
    8613     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 CA     -0.248    3.558
    8614     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 111 CA     -0.257    3.717
    8615     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A THR 183 HA     -0.278    3.038
    8616     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O   3ALN.pdbqt #1/A SER 233 OG     -0.287    2.807
    8617     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A VAL 116 CG2    -0.305    3.615
    8618     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A SER 233 OG     -0.305    3.565
    8619     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A GLY 114 N      -0.308    3.813
    8620     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ALA 112 HN     -0.324    3.084
    8621     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O   3ALN.pdbqt #1/A VAL 116 CG2    -0.327    3.447
    8622     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ALA 129 CB     -0.329    3.909
    8623     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 3HD1   -0.337    3.097
    8624     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL  3ALN.pdbqt #1/A ALA 112 HN     -0.339    3.219
    8625     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 2HD1   -0.352    3.112
    8626     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A LEU 236 2HD1   -0.353    3.233
    8627     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A SER 182 O      -0.357    3.597
    8628     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A GLY 114 O      -0.359    3.599
    8629     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ILE 108 CD1    -0.382    3.842
    8630     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A VAL 116 3HG2   -0.398    3.008
    8631     3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C   3ALN.pdbqt #1/A ALA 129 HB3    -0.400    3.280
    8632    
    8633 
    8634  
    8635 50 contacts 
    8636 
    8637 > hbonds :UNL showDist true radius 0.05 log true saveFile
    8638 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
    8639 > WRM-16.hbonds.txt
    8640 
    8641 The following atoms were skipped as donors/acceptors due to missing heavy-atom
    8642 bond partners: 3ALN.pdbqt #1/A PRO 308 N 
    8643 
    8644    
    8645    
    8646     Finding intermodel H-bonds
    8647     Finding intramodel H-bonds
    8648     Constraints relaxed by 0.4 angstroms and 20 degrees
    8649     Models used:
    8650         1 3ALN.pdbqt
    8651         2.1 3ALN--WRM-16.result.pdbqt
    8652    
    8653     0 H-bonds
    8654     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8655    
    8656 
    8657  
    8658 0 hydrogen bonds found 
    8659 
    8660 > select :UNL
    8661 
    8662 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8663 
    8664 > label sel text "Ligand "
    8665 
    8666 > label height 1
    8667 
    8668 > ~select
    8669 
    8670 Nothing selected 
    8671 
    8672 > 2dlabels text "Binding Energy: -8.7 kcal/mol" color red size 18 xpos .03
    8673 > ypos .95
    8674 
    8675 > 2dlabels text "3ALN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
    8676 
    8677 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
    8678 > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
    8679 > true
    8680 
    8681 > select :UNL
    8682 
    8683 28 atoms, 31 bonds, 1 residue, 1 model selected 
    8684 
    8685 > view sel
    8686 
    8687 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
    8688 > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
    8689 > true
    8690 
    8691 > close
    8692 
    8693 > wait 5
    8694 
    8695 > set bgColor white
    8696 
    8697 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1BJ8.pdbqt
    8698 
    8699 Chain information for 1BJ8.pdbqt #1 
    8700 --- 
    8701 Chain | Description 
    8702 A | No description available 
    8703  
    8704 Opened 1BJ8.pdbqt containing 1 structures (1763 atoms, 1786 bonds) 
    8705 
    8706 > wait 5
    8707 
    8708 > hide surfaces
    8709 
    8710 > hide atoms
    8711 
    8712 > show cartoons
    8713 
    8714 > wait 5
    8715 
    8716 > addh
    8717 
    8718 Summary of feedback from adding hydrogens to 1BJ8.pdbqt #1 
    8719 --- 
    8720 notes | No usable SEQRES records for 1BJ8.pdbqt (#1) chain A; guessing termini
    8721 instead 
    8722 Chain-initial residues that are actual N termini: /A MET 1 
    8723 Chain-initial residues that are not actual N termini: 
    8724 Chain-final residues that are actual C termini: /A ARG 109 
    8725 Chain-final residues that are not actual C termini: 
    8726 53 hydrogen bonds 
    8727 1 hydrogens added 
    8728  
    8729 
    8730 > wait 5
    8731 
    8732 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--
    8733 > WRM-16.result.pdbqt
    8734 
    8735 Summary of feedback from opening
    8736 /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--WRM-16.result.pdbqt 
    8737 --- 
    8738 warnings | Ignored bad PDB record found on line 2 
    8739 REMARK VINA RESULT: -6.1 0.000 0.000 
    8740  
    8741 Ignored bad PDB record found on line 3 
    8742 REMARK 5 active torsions: 
    8743  
    8744 Ignored bad PDB record found on line 4 
    8745 REMARK status: ('A' for Active; 'I' for Inactive) 
    8746  
    8747 Ignored bad PDB record found on line 5 
    8748 REMARK 1 A between atoms: C_9 and O_15 
    8749  
    8750 Ignored bad PDB record found on line 6 
    8751 REMARK 2 A between atoms: C_10 and O_17 
    8752  
    8753 184 messages similar to the above omitted 
    8754  
    8755 Opened 1BJ8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
    8756 bonds) 
    8757 
    8758 > wait 5
    8759 
    8760 > close #2.2-9
    8761 
    8762 > wait 5
    8763 
    8764 > contacts :UNL radius 0.05 log true saveFile
    8765 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
    8766 > WRM-16.contacts.txt
    8767    
    8768    
    8769     Allowed overlap: -0.4
    8770     H-bond overlap reduction: 0.4
    8771     Ignore contacts between atoms separated by 4 bonds or less
    8772     Detect intra-residue contacts: False
    8773     Detect intra-molecule contacts: True
    8774    
    8775     46 contacts
    8776                       atom1                               atom2             overlap  distance
    8777     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HN     0.407    2.473
    8778     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HD1    0.307    2.573
    8779     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 CD1    0.188    3.392
    8780     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 5 HD2     0.101    2.659
    8781     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 5 HD2     0.099    2.661
    8782     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TRP 94 HD1    0.093    2.367
    8783     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 N      0.055    3.450
    8784     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HB1    0.042    2.568
    8785     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 HA     0.032    2.848
    8786     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1BJ8.pdbqt #1/A TYR 93 HE1    0.021    2.859
    8787     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A ARG 84 1HH1   -0.035    2.915
    8788     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 HD1    -0.079    2.959
    8789     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL  1BJ8.pdbqt #1/A TYR 93 CE1    -0.079    3.659
    8790     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HD1    -0.085    2.965
    8791     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A GLY 92 O      -0.136    3.496
    8792     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 3 CG      -0.149    3.609
    8793     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 5 CD      -0.166    3.626
    8794     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HD1    -0.172    2.782
    8795     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 O      -0.174    3.264
    8796     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A ARG 84 1HH1   -0.175    2.235
    8797     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 CE1    -0.177    3.487
    8798     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HB1    -0.200    2.810
    8799     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 HE1    -0.226    2.836
    8800     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 O      -0.231    3.471
    8801     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 3 CB      -0.254    3.714
    8802     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A GLY 92 O      -0.270    3.510
    8803     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 CE1    -0.273    3.733
    8804     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TYR 93 CA     -0.283    3.863
    8805     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TRP 94 CD1    -0.288    3.448
    8806     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 5 HZ2     -0.299    3.059
    8807     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 3 HG2     -0.302    3.062
    8808     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 5 CD      -0.307    3.767
    8809     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 91 O      -0.315    3.555
    8810     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TYR 93 HB2    -0.317    2.777
    8811     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A ARG 84 NH1    -0.328    3.013
    8812     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 HB1    -0.331    2.941
    8813     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 3 CD      -0.332    3.792
    8814     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TYR 93 HD1    -0.338    2.798
    8815     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A LYS 3 HD2     -0.347    3.107
    8816     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 CD1    -0.352    3.662
    8817     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A ARG 84 CZ     -0.358    3.478
    8818     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TYR 93 CB     -0.364    3.524
    8819     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 CB     -0.372    3.682
    8820     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A ARG 84 NH1    -0.385    3.890
    8821     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O   1BJ8.pdbqt #1/A TYR 93 CA     -0.392    3.552
    8822     1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C   1BJ8.pdbqt #1/A TRP 94 O      -0.399    3.489
    8823    
    8824 
    8825  
    8826 46 contacts 
    8827 
    8828 > hbonds :UNL showDist true radius 0.05 log true saveFile
    8829 > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
    8830 > WRM-16.hbonds.txt
    8831    
    8832    
    8833     Finding intermodel H-bonds
    8834     Finding intramodel H-bonds
    8835     Constraints relaxed by 0.4 angstroms and 20 degrees
    8836     Models used:
    8837         1 1BJ8.pdbqt
    8838         2.1 1BJ8--WRM-16.result.pdbqt
    8839    
    8840     1 H-bonds
    8841     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8842     1BJ8.pdbqt #1/A ARG 84 NH1  1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O  1BJ8.pdbqt #1/A ARG 84 1HH1  3.013  2.235
    8843    
    8844103
    8845104