Ticket #16279: Report Log.txt

File Report Log.txt, 7.7 KB (added by johnfranciscortez.jfc@…, 13 months ago)

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1Report Log
2Using Amber 20 recommended default charges and atom types for standard residues
3Assigning partial charges to residue UNL (net charge -1) with am1-bcc method
4Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.8/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\johnf\AppData\Local\Temp\tmpr98g2iik\ante.in.mol2 -fi mol2 -o C:\Users\johnf\AppData\Local\Temp\tmpr98g2iik\ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
5(UNL)
6(UNL) Welcome to antechamber 20.0: molecular input file processor.
7(UNL)
8(UNL) Info: Finished reading file (C:\Users\johnf\AppData\Local\Temp\tmpr98g2iik\ante.in.mol2); atoms read (63), bonds read (66).
9(UNL) Info: Determining atomic numbers from atomic symbols which are case sensitive.
10(UNL) Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
11(UNL) bash.exe: warning: could not find /tmp, please create!
12(UNL)
13(UNL)
14(UNL) Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
15(UNL) bash.exe: warning: could not find /tmp, please create!
16(UNL) Info: Total number of electrons: 242; net charge: -1
17(UNL)
18(UNL) Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out
19(UNL) bash.exe: warning: could not find /tmp, please create!
20
21Contents of sqm.out:
22 --------------------------------------------------------
23 AMBER SQM VERSION 19
24
25 By
26 Ross C. Walker, Michael F. Crowley, Scott Brozell,
27 Tim Giese, Andreas W. Goetz,
28 Tai-Sung Lee and David A. Case
29
30 --------------------------------------------------------
31
32
33--------------------------------------------------------------------------------
34 QM CALCULATION INFO
35--------------------------------------------------------------------------------
36
37| QMMM: Citation for AMBER QMMM Run:
38| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
39
40QMMM: SINGLET STATE CALCULATION
41QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 87
42
43| QMMM: *** Selected Hamiltonian ***
44| QMMM: AM1
45
46| QMMM: *** Parameter sets in use ***
47| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
48| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
49| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
50
51| QMMM: *** SCF convergence criteria ***
52| QMMM: Energy change : 0.1D-07 kcal/mol
53| QMMM: Error matrix |FP-PF| : 0.1D+00 au
54| QMMM: Density matrix change : 0.5D-05
55| QMMM: Maximum number of SCF cycles : 1000
56
57| QMMM: *** Diagonalization Routine Information ***
58| QMMM: Pseudo diagonalizations are allowed.
59| QMMM: Auto diagonalization routine selection is in use.
60| QMMM:
61| QMMM: Timing diagonalization routines:
62| QMMM: norbs = 165
63| QMMM: diag iterations used for timing = 5
64| QMMM:
65| QMMM: Internal diag routine = 0.063975 seconds
66| QMMM: Dspev diag routine = 0.053957 seconds
67| QMMM: Dspevd diag routine = 0.042807 seconds
68| QMMM: Dspevx diag routine = 0.191501 seconds
69| QMMM: Dsyev diag routine = 0.061198 seconds
70| QMMM: Dsyevd diag routine = 0.050449 seconds
71| QMMM: Dsyevr diag routine = 0.050166 seconds
72| QMMM:
73| QMMM: Pseudo diag routine = 0.031799 seconds
74| QMMM:
75| QMMM: Using dspevd routine (diag_routine=3).
76
77 QMMM: QM Region Cartesian Coordinates (*=link atom)
78 QMMM: QM_NO. MM_NO. ATOM X Y Z
79 QMMM: 1 1 C 1.0300 -1.7900 0.0000
80 QMMM: 2 2 C 0.6390 -4.6220 0.0000
81 QMMM: 3 3 C 6.4230 0.8530 0.0000
82 QMMM: 4 4 C 7.4210 0.4920 0.0000
83 QMMM: 5 5 C 5.3340 -1.6190 0.0000
84 QMMM: 6 6 C 2.8180 -2.0210 0.0000
85 QMMM: 7 7 C 3.6560 0.2980 0.0000
86 QMMM: 8 8 C 1.6520 -3.3190 0.0000
87 QMMM: 9 9 C 2.1580 -2.6670 0.0000
88 QMMM: 10 10 C 1.9630 -4.0830 0.0000
89 QMMM: 11 11 C 2.1240 -0.4600 0.0000
90 QMMM: 12 12 C 4.5220 -1.7640 0.0000
91 QMMM: 13 13 C 6.9590 -1.3290 0.0000
92 QMMM: 14 14 C 6.1460 -1.4740 0.0000
93 QMMM: 15 15 C 3.7100 -1.9090 0.0000
94 QMMM: 16 16 C 2.8070 0.0040 0.0000
95 QMMM: 17 17 C 5.3630 0.5640 0.0000
96 QMMM: 18 18 C 1.8470 -1.9030 0.0000
97 QMMM: 19 19 C 1.4560 -4.7340 0.0000
98 QMMM: 20 20 C 2.3540 -1.2520 0.0000
99 QMMM: 21 21 C 4.8030 -0.9880 0.0000
100 QMMM: 22 22 C 4.5510 0.4180 0.0000
101 QMMM: 23 23 C 5.8950 -0.0670 0.0000
102 QMMM: 24 24 C 7.2390 -0.5530 0.0000
103 QMMM: 25 25 C 4.2710 -0.3580 0.0000
104 QMMM: 26 26 C 1.7670 -5.4980 0.0000
105 QMMM: 27 27 C 6.7070 0.0780 0.0000
106 QMMM: 28 28 C 5.6150 -0.8430 0.0000
107 QMMM: 29 29 C 3.1780 -1.2790 0.0000
108 QMMM: 30 30 C 3.4590 -0.5030 0.0000
109 QMMM: 31 31 O 4.0190 1.0490 0.0000
110 QMMM: 32 32 O 8.0510 -0.4070 0.0000
111 QMMM: 33 33 O 2.5850 -5.6110 0.0000
112 QMMM: 34 34 O 1.2610 -6.1500 0.0000
113 QMMM: 35 35 H 0.5820 -3.1710 0.0000
114 QMMM: 36 36 H 3.2280 -2.8150 0.0000
115 QMMM: 37 37 H 3.0330 -4.2310 0.0000
116 QMMM: 38 38 H 1.1090 -0.0930 0.0000
117 QMMM: 39 39 H 5.2180 -2.5900 0.0000
118 QMMM: 40 40 H 7.6550 -2.1540 0.0000
119 QMMM: 41 41 H 5.7790 -2.4900 0.0000
120 QMMM: 42 42 H 3.3430 -2.9250 0.0000
121 QMMM: 43 43 H 2.8420 1.0830 0.0000
122 QMMM: 44 44 H 5.7300 1.5790 0.0000
123 QMMM: 45 45 H 0.3670 -2.6430 0.0000
124 QMMM: 46 46 H 0.6230 -0.7900 0.0000
125 QMMM: 47 47 H 0.2320 -3.6210 0.0000
126 QMMM: 48 48 H -0.0240 -5.4740 0.0000
127 QMMM: 49 49 H 7.2630 1.5480 0.0000
128 QMMM: 50 50 H 5.8160 1.0160 -0.8900
129 QMMM: 51 51 H 5.8150 1.0170 0.8900
130 QMMM: 52 52 H 7.2190 1.5630 0.0000
131 QMMM: 53 53 H 7.9920 0.2300 -0.8900
132 QMMM: 54 54 H 7.9930 0.2300 0.8900
133 QMMM: 55 55 H 6.1770 -2.3100 0.0000
134 QMMM: 56 56 H 4.7280 -1.7860 0.8900
135 QMMM: 57 57 H 4.7270 -1.7860 -0.8900
136 QMMM: 58 58 H 3.5840 -2.7970 0.0000
137 QMMM: 59 59 H 2.1980 -2.1240 0.8900
138 QMMM: 60 60 H 2.1970 -2.1240 -0.8900
139 QMMM: 61 61 H 2.7460 0.8970 0.0000
140 QMMM: 62 62 H 4.2420 0.5280 0.8900
141
142Failure running ANTECHAMBER for residue UNL
143Check reply log for details