Add Charge failure

[chinmairayidi@…]

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

6vei_top1.pdb​

[chinmairayidi@…]

Added by email2trac

[Eric Pettersen]

Works on my Mac. I don't see an error in the sqm.out output. Need to try on a Windows system.

[Eric Pettersen]

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.