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Opened 23 months ago
Closed 23 months ago
#14435 closed defect (not a bug)
Charge failure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Uploaded the "NTG.mol2" file. Selected "Tools, Structure editing, Dock Prep"
Selected Pubchem:89909564 #1.1 and clicked "OK" for all the following windows.
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/olive/Desktop/Wyoming/Information/Molegro/Compund Model
> files/Focus compounds/NTG.mol2"
Opened NTG.mol2 containing 2 structures (140 atoms, 146 bonds)
> ui tool show "Dock Prep"
> hide #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> ui tool show "Dock Prep"
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to pubchem:89909564 #1.1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
0 hydrogens added
Closest equivalent command: addcharge #1.1 standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.in.mol2 -fi mol2 -o
C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(C:\Users\olive\AppData\Local\Temp\tmppi32dmig\ante.in.mol2); atoms read (70),
bonds read (73).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: Total number of electrons: 284; net charge: 0`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `/usr/bin/antechamber: Fatal Error!`
(UNL) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =104
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 184
| QMMM: diag iterations used for timing = 5
| QMMM:
| QMMM: Internal diag routine = 0.081402 seconds
| QMMM: Dspev diag routine = 0.071848 seconds
| QMMM: Dspevd diag routine = 0.055359 seconds
| QMMM: Dspevx diag routine = 0.238989 seconds
| QMMM: Dsyev diag routine = 0.078126 seconds
| QMMM: Dsyevd diag routine = 0.058881 seconds
| QMMM: Dsyevr diag routine = 0.060725 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.035736 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O 6.8670 -1.5870 0.0000
QMMM: 2 2 O 5.5580 0.3640 0.0000
QMMM: 3 3 O 5.1350 -1.5870 0.0000
QMMM: 4 4 O 6.8670 -3.5870 0.0000
QMMM: 5 5 O 5.1350 -4.5870 0.0000
QMMM: 6 6 O 3.4030 -3.5870 0.0000
QMMM: 7 7 O 4.8720 -0.4830 0.0000
QMMM: 8 8 O 2.5370 -2.0870 0.0000
QMMM: 9 9 O 10.1360 -3.4700 0.0000
QMMM: 10 10 O 10.4450 3.2470 0.0000
QMMM: 11 11 O 8.6500 -4.8090 0.0000
QMMM: 12 12 O 8.9590 4.5850 0.0000
QMMM: 13 13 C 6.8670 -0.5870 0.0000
QMMM: 14 14 C 7.1760 0.3640 0.0000
QMMM: 15 15 C 6.0010 -2.0870 0.0000
QMMM: 16 16 C 7.8180 -0.8960 0.0000
QMMM: 17 17 C 6.3670 0.9520 0.0000
QMMM: 18 18 C 8.1270 0.6730 0.0000
QMMM: 19 19 C 6.0010 -3.0870 0.0000
QMMM: 20 20 C 5.8670 -0.5870 0.0000
QMMM: 21 21 C 5.1350 -3.5870 0.0000
QMMM: 22 22 C 4.2690 -3.0870 0.0000
QMMM: 23 23 C 4.2690 -2.0870 0.0000
QMMM: 24 24 C 8.0260 -1.8740 0.0000
QMMM: 25 25 C 8.3350 1.6510 0.0000
QMMM: 26 26 C 3.4030 -1.5870 0.0000
QMMM: 27 27 C 8.9770 -2.1830 0.0000
QMMM: 28 28 C 7.2830 -2.5430 0.0000
QMMM: 29 29 C 9.2860 1.9600 0.0000
QMMM: 30 30 C 7.5920 2.3200 0.0000
QMMM: 31 31 C 9.1850 -3.1620 0.0000
QMMM: 32 32 C 7.4910 -3.5220 0.0000
QMMM: 33 33 C 9.4940 2.9380 0.0000
QMMM: 34 34 C 7.8000 3.2980 0.0000
QMMM: 35 35 C 8.4420 -3.8310 0.0000
QMMM: 36 36 C 8.7510 3.6070 0.0000
QMMM: 37 37 C 10.8790 -2.8010 0.0000
QMMM: 38 38 C 10.6530 4.2250 0.0000
QMMM: 39 39 H 7.2730 0.9760 0.0000
QMMM: 40 40 H 6.0010 -1.4670 0.0000
QMMM: 41 41 H 8.4380 -0.8750 0.0000
QMMM: 42 42 H 7.9040 -0.2820 0.0000
QMMM: 43 43 H 6.7820 1.4120 0.0000
QMMM: 44 44 H 5.9520 1.4120 0.0000
QMMM: 45 45 H 8.2130 0.0590 0.0000
QMMM: 46 46 H 8.7470 0.6510 0.0000
QMMM: 47 47 H 6.0010 -3.7070 0.0000
QMMM: 48 48 H 4.5980 -3.8970 0.0000
QMMM: 49 49 H 4.2690 -3.7070 0.0000
QMMM: 50 50 H 4.2690 -1.4670 0.0000
QMMM: 51 51 H 3.8010 -1.1120 0.0000
QMMM: 52 52 H 3.0040 -1.1120 0.0000
QMMM: 53 53 H 6.8670 -4.2070 0.0000
QMMM: 54 54 H 4.5980 -4.8970 0.0000
QMMM: 55 55 H 3.4030 -4.2070 0.0000
QMMM: 56 56 H 9.4380 -1.7680 0.0000
QMMM: 57 57 H 6.6930 -2.3520 0.0000
QMMM: 58 58 H 9.7470 1.5450 0.0000
QMMM: 59 59 H 7.0020 2.1290 0.0000
QMMM: 60 60 H 7.0300 -3.9370 0.0000
QMMM: 61 61 H 2.0000 -1.7770 0.0000
QMMM: 62 62 H 7.3390 3.7130 0.0000
QMMM: 63 63 H 9.2390 -5.0000 0.0000
QMMM: 64 64 H 8.4980 5.0000 0.0000
QMMM: 65 65 H 11.2940 -3.2620 0.0000
QMMM: 66 66 H 11.3400 -2.3860 0.0000
QMMM: 67 67 H 10.4640 -2.3410 0.0000
QMMM: 68 68 H 11.2590 4.0960 0.0000
QMMM: 69 69 H 10.7820 4.8320 0.0000
QMMM: 70 70 H 10.0460 4.3540 0.0000
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1974E+07 DeltaE = 0.2157E+01 DeltaP = 0.4873E-01
QMMM: Smallest DeltaE = -0.3257E-02 DeltaP = 0.1499E-01 Step = 26
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges
add_nonstandard_res_charges(self.session, residues, charge, method=method)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 319, in
add_nonstandard_res_charges
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge
raise ChargeError(ante_failure_msg)
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge
raise ChargeError(ante_failure_msg)
See log for complete Python traceback.
> ui tool show "Dock Prep"
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to pubchem:89909564 #1.1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
0 hydrogens added
Closest equivalent command: addcharge #1.1 standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.in.mol2 -fi mol2 -o
C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(C:\Users\olive\AppData\Local\Temp\tmp7f9n415z\ante.in.mol2); atoms read (70),
bonds read (73).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: Total number of electrons: 284; net charge: 0`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `/usr/bin/antechamber: Fatal Error!`
(UNL) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =104
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 184
| QMMM: diag iterations used for timing = 5
| QMMM:
| QMMM: Internal diag routine = 0.079216 seconds
| QMMM: Dspev diag routine = 0.071098 seconds
| QMMM: Dspevd diag routine = 0.054125 seconds
| QMMM: Dspevx diag routine = 0.236499 seconds
| QMMM: Dsyev diag routine = 0.075961 seconds
| QMMM: Dsyevd diag routine = 0.058941 seconds
| QMMM: Dsyevr diag routine = 0.062282 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.036449 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O 6.8670 -1.5870 0.0000
QMMM: 2 2 O 5.5580 0.3640 0.0000
QMMM: 3 3 O 5.1350 -1.5870 0.0000
QMMM: 4 4 O 6.8670 -3.5870 0.0000
QMMM: 5 5 O 5.1350 -4.5870 0.0000
QMMM: 6 6 O 3.4030 -3.5870 0.0000
QMMM: 7 7 O 4.8720 -0.4830 0.0000
QMMM: 8 8 O 2.5370 -2.0870 0.0000
QMMM: 9 9 O 10.1360 -3.4700 0.0000
QMMM: 10 10 O 10.4450 3.2470 0.0000
QMMM: 11 11 O 8.6500 -4.8090 0.0000
QMMM: 12 12 O 8.9590 4.5850 0.0000
QMMM: 13 13 C 6.8670 -0.5870 0.0000
QMMM: 14 14 C 7.1760 0.3640 0.0000
QMMM: 15 15 C 6.0010 -2.0870 0.0000
QMMM: 16 16 C 7.8180 -0.8960 0.0000
QMMM: 17 17 C 6.3670 0.9520 0.0000
QMMM: 18 18 C 8.1270 0.6730 0.0000
QMMM: 19 19 C 6.0010 -3.0870 0.0000
QMMM: 20 20 C 5.8670 -0.5870 0.0000
QMMM: 21 21 C 5.1350 -3.5870 0.0000
QMMM: 22 22 C 4.2690 -3.0870 0.0000
QMMM: 23 23 C 4.2690 -2.0870 0.0000
QMMM: 24 24 C 8.0260 -1.8740 0.0000
QMMM: 25 25 C 8.3350 1.6510 0.0000
QMMM: 26 26 C 3.4030 -1.5870 0.0000
QMMM: 27 27 C 8.9770 -2.1830 0.0000
QMMM: 28 28 C 7.2830 -2.5430 0.0000
QMMM: 29 29 C 9.2860 1.9600 0.0000
QMMM: 30 30 C 7.5920 2.3200 0.0000
QMMM: 31 31 C 9.1850 -3.1620 0.0000
QMMM: 32 32 C 7.4910 -3.5220 0.0000
QMMM: 33 33 C 9.4940 2.9380 0.0000
QMMM: 34 34 C 7.8000 3.2980 0.0000
QMMM: 35 35 C 8.4420 -3.8310 0.0000
QMMM: 36 36 C 8.7510 3.6070 0.0000
QMMM: 37 37 C 10.8790 -2.8010 0.0000
QMMM: 38 38 C 10.6530 4.2250 0.0000
QMMM: 39 39 H 7.2730 0.9760 0.0000
QMMM: 40 40 H 6.0010 -1.4670 0.0000
QMMM: 41 41 H 8.4380 -0.8750 0.0000
QMMM: 42 42 H 7.9040 -0.2820 0.0000
QMMM: 43 43 H 6.7820 1.4120 0.0000
QMMM: 44 44 H 5.9520 1.4120 0.0000
QMMM: 45 45 H 8.2130 0.0590 0.0000
QMMM: 46 46 H 8.7470 0.6510 0.0000
QMMM: 47 47 H 6.0010 -3.7070 0.0000
QMMM: 48 48 H 4.5980 -3.8970 0.0000
QMMM: 49 49 H 4.2690 -3.7070 0.0000
QMMM: 50 50 H 4.2690 -1.4670 0.0000
QMMM: 51 51 H 3.8010 -1.1120 0.0000
QMMM: 52 52 H 3.0040 -1.1120 0.0000
QMMM: 53 53 H 6.8670 -4.2070 0.0000
QMMM: 54 54 H 4.5980 -4.8970 0.0000
QMMM: 55 55 H 3.4030 -4.2070 0.0000
QMMM: 56 56 H 9.4380 -1.7680 0.0000
QMMM: 57 57 H 6.6930 -2.3520 0.0000
QMMM: 58 58 H 9.7470 1.5450 0.0000
QMMM: 59 59 H 7.0020 2.1290 0.0000
QMMM: 60 60 H 7.0300 -3.9370 0.0000
QMMM: 61 61 H 2.0000 -1.7770 0.0000
QMMM: 62 62 H 7.3390 3.7130 0.0000
QMMM: 63 63 H 9.2390 -5.0000 0.0000
QMMM: 64 64 H 8.4980 5.0000 0.0000
QMMM: 65 65 H 11.2940 -3.2620 0.0000
QMMM: 66 66 H 11.3400 -2.3860 0.0000
QMMM: 67 67 H 10.4640 -2.3410 0.0000
QMMM: 68 68 H 11.2590 4.0960 0.0000
QMMM: 69 69 H 10.7820 4.8320 0.0000
QMMM: 70 70 H 10.0460 4.3540 0.0000
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1974E+07 DeltaE = 0.2157E+01 DeltaP = 0.4873E-01
QMMM: Smallest DeltaE = -0.3257E-02 DeltaP = 0.1499E-01 Step = 26
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges
add_nonstandard_res_charges(self.session, residues, charge, method=method)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 319, in
add_nonstandard_res_charges
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge
raise ChargeError(ante_failure_msg)
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL
Check reply log for details
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 602, in nonstd_charge
raise ChargeError(ante_failure_msg)
See log for complete Python traceback.
> ui tool show "Dock Prep"
OpenGL version: 3.3.0 - Build 27.20.100.8729
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: LENOVO
Model: 81EK
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,458,571,776
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: de-DE
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
File attachment: NTG.mol2
Attachments (1)
Change History (3)
by , 23 months ago
comment:1 by , 23 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Charge failure |
Reported by Oliver Trunschke
comment:2 by , 23 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
Hi Oliver,
It looks like your NTG.mol2 file is a two-dimensional representation of the molecule rather than a three-dimensional one. I wouldn't necessarily expect a two-dimensional representation to work, and if it did the charges likely would not be very good because the computation depends on spatial proximity of atoms and the electronic structure implied by bond geometry.
It seems your structure is for PubChem CID 89909564. Normally you could open the 3-dimensional structure for that entry in ChimeraX with the command "open pubchem:89909564", but there seems to be some problem with PubChem for that entry. Nonetheless you could open the entry with its IUPAC name instead:
open iupac:3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxolan-2-one
That produces a three-dimensional structure that Add Charge works fine with. I would also suggest upgrading your version of ChimeraX to 1.7, which has a more robust version of Add Charge where if the first charge computation fails, it falls back to a slower more exhaustive computation.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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