![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16450 closed defect (not a bug)
Add Charge failure
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-10-10.0.26100
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)chimera not responding
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\Chinmai Rayidi\OneDrive\Desktop\6vei\6vei_top1\6vei_top1.pdb"
> format pdb
6vei_top1.pdb title:
Crystal structure of human cytosolic isocitrate dehydrogenase (IDH1) R132H
mutant In complex with nadph and Ag-881 (vorasidenib) inhibitor [more info...]
Chain information for 6vei_top1.pdb #1
---
Chain | Description
B | No description available
Non-standard residues in 6vei_top1.pdb #1
---
UNK — (UNK)
> select /B
6581 atoms, 6652 bonds, 417 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 6vei_top1.pdb #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:
1 hydrogen bonds
0 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNK (net charge -1) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\CHINMA~1\AppData\Local\Temp\tmpg1lpr13o\ante.in.mol2 -fi mol2 -o
C:\Users\CHINMA~1\AppData\Local\Temp\tmpg1lpr13o\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n
(UNK) ``
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`
(UNK) ``
(UNK) `Info: Finished reading file
(C:\Users\CHINMA~1\AppData\Local\Temp\tmpg1lpr13o\ante.in.mol2); atoms read
(143), bonds read (143).`
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) ``
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) `Info: Total number of electrons: 484; net charge: -1`
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
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 =177
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| 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 = 326
| QMMM: diag iterations used for timing = 2
| QMMM:
| QMMM: Internal diag routine = 0.137065 seconds
| QMMM: Dspev diag routine = 0.117363 seconds
| QMMM: Dspevd diag routine = 0.080436 seconds
| QMMM: Dspevx diag routine = 0.270740 seconds
| QMMM: Dsyev diag routine = 0.109481 seconds
| QMMM: Dsyevd diag routine = 0.080491 seconds
| QMMM: Dsyevr diag routine = 0.086033 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.083425 seconds
| QMMM: Pseudo diagonalization appears to be slower than regular
| QMMM: diagonalization. Setting pseudo_diag=0 for optimum performance.
| 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 C 27.4460 25.5080 22.9340
QMMM: 2 2 C 26.5110 24.4540 23.5410
QMMM: 3 3 C 26.2150 23.2750 22.6010
QMMM: 4 4 C 27.3750 22.2740 22.4750
QMMM: 5 5 C 27.0220 21.0920 21.5680
QMMM: 6 6 C 28.1370 20.0610 21.5210
QMMM: 7 7 C 28.9380 19.7630 20.4800
QMMM: 8 8 C 28.9240 20.3790 19.0940
QMMM: 9 9 C 28.8090 19.2790 18.0580
QMMM: 10 10 C 29.6670 19.0020 17.0600
QMMM: 11 11 C 30.9530 19.7310 16.7190
QMMM: 12 12 C 32.1620 18.8680 17.0330
QMMM: 13 13 C 33.1480 19.1660 17.9050
QMMM: 14 14 C 33.2030 20.4050 18.7780
QMMM: 15 15 C 33.6780 21.6540 18.0190
QMMM: 16 16 C 33.2120 22.9650 18.6700
QMMM: 17 17 C 33.8590 23.2470 20.0330
QMMM: 18 18 C 33.2810 24.5180 20.6850
QMMM: 19 19 C 33.7790 24.7810 22.1170
QMMM: 20 20 C 33.3700 23.6790 23.0960
QMMM: 21 21 O 34.2050 23.0690 23.7470
QMMM: 22 22 O 32.0520 23.4620 23.1350
QMMM: 23 23 C 31.5440 22.3240 23.8220
QMMM: 24 24 C 31.0330 21.3560 22.7420
QMMM: 25 25 O 32.0510 20.4250 22.3890
QMMM: 26 26 C 32.1300 19.2520 23.0410
QMMM: 27 27 O 31.3270 18.8370 23.8710
QMMM: 28 28 C 33.3460 18.4200 22.6420
QMMM: 29 29 C 33.0770 17.5570 21.4000
QMMM: 30 30 C 34.3080 16.7640 20.9290
QMMM: 31 31 C 34.8210 15.7710 21.9880
QMMM: 32 32 C 35.8870 14.7990 21.4470
QMMM: 33 33 C 36.3800 13.7950 22.5020
QMMM: 34 34 C 37.4140 14.3850 23.4680
QMMM: 35 35 C 37.7960 13.3940 24.5780
QMMM: 36 36 C 38.9940 13.8750 25.4050
QMMM: 37 37 C 39.2750 12.9820 26.6010
QMMM: 38 38 C 39.7140 13.3670 27.8130
QMMM: 39 39 C 40.0490 14.7760 28.2820
QMMM: 40 40 C 39.3390 15.1300 29.6030
QMMM: 41 41 C 39.8340 16.4570 30.2120
QMMM: 42 42 C 39.2260 16.7260 31.6020
QMMM: 43 43 C 39.8260 17.9430 32.3340
QMMM: 44 44 C 39.4040 19.3020 31.7540
QMMM: 45 45 C 30.4260 22.7610 24.7840
QMMM: 46 46 O 30.8730 23.4780 25.9200
QMMM: 47 47 P 32.2830 23.0810 26.7960
QMMM: 48 48 O 33.4060 23.8610 26.2410
QMMM: 49 49 O 32.3850 21.6040 26.8950
QMMM: 50 50 O 31.9160 23.6730 28.3400
QMMM: 51 51 C 32.9140 23.9710 29.3000
QMMM: 52 52 C 33.7410 25.2240 28.9420
QMMM: 53 53 O 32.8100 26.2380 28.6330
QMMM: 54 54 C 34.7040 25.6630 30.0760
QMMM: 55 55 O 35.8050 24.7700 30.1010
QMMM: 56 56 C 34.0350 25.6630 31.4720
QMMM: 57 57 O 35.0210 25.8790 32.4670
QMMM: 58 58 C 33.3010 24.3300 31.7650
QMMM: 59 59 O 32.6440 24.3510 33.0150
QMMM: 60 60 C 32.2460 24.0250 30.6890
QMMM: 61 61 O 31.2570 25.0480 30.7300
QMMM: 62 62 H 27.6240 26.3200 23.6390
QMMM: 63 63 H 27.0190 25.9400 22.0290
QMMM: 64 64 H 28.4110 25.0740 22.6680
QMMM: 65 65 H 26.9300 24.0860 24.4790
QMMM: 66 66 H 25.5700 24.9400 23.8040
QMMM: 67 67 H 25.3420 22.7440 22.9770
QMMM: 68 68 H 25.9360 23.6510 21.6140
QMMM: 69 69 H 28.2570 22.7790 22.0830
QMMM: 70 70 H 27.6440 21.9070 23.4670
QMMM: 71 71 H 26.1290 20.5890 21.9460
QMMM: 72 72 H 26.7640 21.4650 20.5790
QMMM: 73 73 H 28.2950 19.5220 22.4420
QMMM: 74 74 H 29.6960 19.0080 20.6360
QMMM: 75 75 H 28.0960 21.0720 18.9600
QMMM: 76 76 H 29.8370 20.9640 18.9780
QMMM: 77 77 H 27.9310 18.6570 18.1510
QMMM: 78 78 H 29.4370 18.1660 16.4160
QMMM: 79 79 H 30.9500 19.9490 15.6480
QMMM: 80 80 H 31.0090 20.7010 17.2080
QMMM: 81 81 H 32.2070 17.9320 16.4920
QMMM: 82 82 H 33.9750 18.4820 18.0040
QMMM: 83 83 H 32.2050 20.5700 19.1820
QMMM: 84 84 H 33.8500 20.2070 19.6330
QMMM: 85 85 H 34.7570 21.6540 17.8700
QMMM: 86 86 H 33.2490 21.6210 17.0240
QMMM: 87 87 H 33.4130 23.7960 17.9950
QMMM: 88 88 H 32.1280 22.9310 18.7830
QMMM: 89 89 H 33.6920 22.3880 20.6830
QMMM: 90 90 H 34.9410 23.3380 19.9220
QMMM: 91 91 H 33.5210 25.3860 20.0650
QMMM: 92 92 H 32.1950 24.4480 20.7000
QMMM: 93 93 H 34.8680 24.8440 22.1120
QMMM: 94 94 H 33.4080 25.7380 22.4840
QMMM: 95 95 H 32.3100 21.8040 24.4010
QMMM: 96 96 H 30.1500 20.8320 23.1040
QMMM: 97 97 H 30.7160 21.9030 21.8520
QMMM: 98 98 H 34.1950 19.0770 22.4640
QMMM: 99 99 H 33.6140 17.7890 23.4890
QMMM: 100 100 H 32.2560 16.8650 21.6010
QMMM: 101 101 H 32.7360 18.1930 20.5840
QMMM: 102 102 H 34.0370 16.2260 20.0230
QMMM: 103 103 H 35.1080 17.4470 20.6450
QMMM: 104 104 H 35.2270 16.3220 22.8360
QMMM: 105 105 H 33.9820 15.1900 22.3710
QMMM: 106 106 H 35.4470 14.2380 20.6230
QMMM: 107 107 H 36.7320 15.3500 21.0310
QMMM: 108 108 H 35.5290 13.3950 23.0540
QMMM: 109 109 H 36.8350 12.9480 21.9880
QMMM: 110 110 H 38.2980 14.6760 22.9010
QMMM: 111 111 H 37.0330 15.2990 23.9240
QMMM: 112 112 H 36.9350 13.2360 25.2300
QMMM: 113 113 H 38.0340 12.4250 24.1370
QMMM: 114 114 H 39.8870 13.8760 24.7740
QMMM: 115 115 H 38.8210 14.9020 25.7190
QMMM: 116 116 H 39.1100 11.9290 26.4310
QMMM: 117 117 H 39.8580 12.5970 28.5560
QMMM: 118 118 H 41.1290 14.8150 28.4260
QMMM: 119 119 H 39.8220 15.5220 27.5230
QMMM: 120 120 H 38.2610 15.1770 29.4360
QMMM: 121 121 H 39.5130 14.3270 30.3210
QMMM: 122 122 H 40.9200 16.4320 30.3060
QMMM: 123 123 H 39.6010 17.2820 29.5420
QMMM: 124 124 H 38.1410 16.8380 31.5270
QMMM: 125 125 H 39.3870 15.8460 32.2310
QMMM: 126 126 H 39.5250 17.9110 33.3810
QMMM: 127 127 H 40.9160 17.8700 32.3310
QMMM: 128 128 H 39.8810 20.1180 32.3000
QMMM: 129 129 H 39.6990 19.3990 30.7100
QMMM: 130 130 H 38.3250 19.4470 31.8180
QMMM: 131 131 H 29.6960 23.3760 24.2580
QMMM: 132 132 H 29.8920 21.8820 25.1520
QMMM: 133 133 H 33.5970 23.1190 29.3060
QMMM: 134 134 H 34.3440 25.0730 28.0500
QMMM: 135 135 H 31.9480 25.8950 28.8760
QMMM: 136 136 H 35.1020 26.6630 29.8650
QMMM: 137 137 H 36.2770 24.9310 30.9080
QMMM: 138 138 H 33.3350 26.4970 31.5240
QMMM: 139 139 H 35.5980 26.5950 32.2180
QMMM: 140 140 H 34.0450 23.5260 31.7840
QMMM: 141 141 H 31.8200 24.7950 32.8890
QMMM: 142 142 H 31.7610 23.0680 30.8930
QMMM: 143 143 H 31.6910 25.8710 30.8560
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -817.8362 kcal/mol 0.4683 kcal/(mol*A)
xmin 20 -823.6334 kcal/mol 0.7473 kcal/(mol*A)
xmin 30 -829.2963 kcal/mol 0.3532 kcal/(mol*A)
xmin 40 -832.3299 kcal/mol 0.3250 kcal/(mol*A)
xmin 50 -834.6491 kcal/mol 0.2287 kcal/(mol*A)
xmin 60 -836.8347 kcal/mol 0.4947 kcal/(mol*A)
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 330, 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 634, in nonstd_charge
raise ChargeError(ante_failure_msg)
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNK
Check reply log for details
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNK
Check reply log for details
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 634, in nonstd_charge
raise ChargeError(ante_failure_msg)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.101.1404
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.2
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Acer
Model: Aspire A515-56
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 12,653,486,080
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
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: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
File attachment: 6vei_top1.pdb
Attachments (1)
Change History (3)
by , 10 months ago
| Attachment: | 6vei_top1.pdb added |
|---|
comment:1 by , 10 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Add Charge failure |
Works on my Mac. I don't see an error in the sqm.out output. Need to try on a Windows system.
comment:2 by , 10 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
The semi-empirical program (sqm) that is computing these charges for ChimeraX is quite slow for a structure as large as your ligand. It takes several minutes to finish. You could use the Gasteiger charge method in Add Charge rather than AM1-BCC, which will be considerably faster, at the cost of a little bit of accuracy.
Note:
See TracTickets
for help on using tickets.
Added by email2trac