Charge failure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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/HP/Desktop/5fu Vs CDs/1d3c-gamma cd pre.pdb"

Summary of feedback from opening C:/Users/HP/Desktop/5fu Vs CDs/1d3c-gamma cd
pre.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2024-03-24T17:40:53Z  
  

> 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 1d3c-gamma cd pre.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:  
50 hydrogen bonds  
276 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 MPD (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\HP\AppData\Local\Temp\tmp8xc8zctw\ante.in.mol2 -fi mol2 -o
C:\Users\HP\AppData\Local\Temp\tmp8xc8zctw\ante.out.mol2 -fo mol2 -c bcc -nc 0
-j 5 -s 2 -dr n  
(MPD) ``  
(MPD) `Welcome to antechamber 20.0: molecular input file processor.`  
(MPD) ``  
(MPD) `Info: Finished reading file
(C:\Users\HP\AppData\Local\Temp\tmp8xc8zctw\ante.in.mol2); atoms read (22),
bonds read (21).`  
(MPD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(MPD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(MPD) `bash.exe: warning: could not find /tmp, please create!`  
(MPD) ``  
(MPD) ``  
(MPD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(MPD) `bash.exe: warning: could not find /tmp, please create!`  
(MPD) `Info: Total number of electrons: 66; net charge: 0`  
(MPD) ``  
(MPD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(MPD) `bash.exe: warning: could not find /tmp, please create!`  
(MPD) ``  
(MPD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(MPD) `bash.exe: warning: could not find /tmp, please create!`  
(MPD) ``  
(MPD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(MPD) `bash.exe: warning: could not find /tmp, please create!`  
(MPD) ``  
Charges for residue MPD determined  
Assigning partial charges to residue GLC+GLC (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\HP\AppData\Local\Temp\tmp6p5bfhtg\ante.in.mol2 -fi mol2 -o
C:\Users\HP\AppData\Local\Temp\tmp6p5bfhtg\ante.out.mol2 -fo mol2 -c bcc -nc 0
-j 5 -s 2 -dr n  
(GLC+GLC) ``  
(GLC+GLC) `Welcome to antechamber 20.0: molecular input file processor.`  
(GLC+GLC) ``  
(GLC+GLC) `Info: Finished reading file
(C:\Users\HP\AppData\Local\Temp\tmp6p5bfhtg\ante.in.mol2); atoms read (45),
bonds read (46).`  
(GLC+GLC) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GLC+GLC) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GLC+GLC) `bash.exe: warning: could not find /tmp, please create!`  
(GLC+GLC) ``  
(GLC+GLC) ``  
(GLC+GLC) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GLC+GLC) `bash.exe: warning: could not find /tmp, please create!`  
(GLC+GLC) `Info: Total number of electrons: 182; net charge: 0`  
(GLC+GLC) ``  
(GLC+GLC) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(GLC+GLC) `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 = 68
    
    | 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: 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 =      114
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.039878 seconds
    | QMMM:                 Dspev diag routine = 0.033299 seconds
    | QMMM:                Dspevd diag routine = 0.024734 seconds
    | QMMM:                Dspevx diag routine = 0.134148 seconds
    | QMMM:                 Dsyev diag routine = 0.038247 seconds
    | QMMM:                Dsyevd diag routine = 0.028824 seconds
    | QMMM:                Dsyevr diag routine = 0.033132 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.014446 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      C       61.7740  102.5320   10.0930
      QMMM:     2        2      C       61.2280  101.6800   11.2020
      QMMM:     3        3      C       62.0250  100.4010   11.3160
      QMMM:     4        4      C       62.0550   99.7200    9.9620
      QMMM:     5        5      C       62.6010  100.6470    8.8820
      QMMM:     6        6      C       62.4700  100.0220    7.5140
      QMMM:     7        7      O       63.0490  102.9480   10.4190
      QMMM:     8        8      O       61.2890  102.3920   12.4400
      QMMM:     9        9      O       61.4110   99.5650   12.2860
      QMMM:    10       10      O       62.9140   98.5740   10.0720
      QMMM:    11       11      O       61.7420  101.7870    8.8740
      QMMM:    12       12      O       63.3010  100.7330    6.5940
      QMMM:    13       13      C       62.3090   97.3050    9.9810
      QMMM:    14       14      C       62.8700   96.4520   11.0950
      QMMM:    15       15      C       64.3480   96.2330   10.8940
      QMMM:    16       16      C       64.6410   95.7130    9.4990
      QMMM:    17       17      C       63.9800   96.5780    8.4430
      QMMM:    18       18      C       64.0830   95.9500    7.0840
      QMMM:    19       19      O       62.6390   97.1030   12.3360
      QMMM:    20       20      O       64.8520   95.2640   11.8160
      QMMM:    21       21      O       66.0300   95.7850    9.2170
      QMMM:    22       22      O       62.5850   96.7240    8.7150
      QMMM:    23       23      O       63.6190   96.8060    6.0370
      QMMM:    24       24      H       61.1380  103.4100    9.9820
      QMMM:    25       25      H       60.1890  101.4340   10.9830
      QMMM:    26       26      H       63.0430  100.6340   11.6290
      QMMM:    27       27      H       61.0490   99.3980    9.6930
      QMMM:    28       28      H       63.6330  100.9310    9.0900
      QMMM:    29       29      H       62.7830   98.9790    7.5580
      QMMM:    30       30      H       61.4320  100.0780    7.1860
      QMMM:    31       31      H       61.2310   97.4060   10.1080
      QMMM:    32       32      H       62.3620   95.4870   11.0970
      QMMM:    33       33      H       64.8740   97.1760   11.0430
      QMMM:    34       34      H       64.2960   94.6830    9.4060
      QMMM:    35       35      H       64.4530   97.5600    8.4280
      QMMM:    36       36      H       65.1270   95.7030    6.8940
      QMMM:    37       37      H       63.4960   95.0310    7.0750
      QMMM:    38       38      H       61.7730   98.6780   12.2200
      QMMM:    39       39      H       62.0760   96.5530   12.8860
      QMMM:    40       40      H       63.3990  103.4930    9.7100
      QMMM:    41       41      H       60.9220  101.8480   13.1400
      QMMM:    42       42      H       63.2220  100.3400    5.7210
      QMMM:    43       43      H       64.6850   95.5590   12.7140
      QMMM:    44       44      H       66.5140   95.2540    9.8540
      QMMM:    45       45      H       63.7070   96.3570    5.1930
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10     -529.8137 kcal/mol        0.6054 kcal/(mol*A)
    xmin    20     -531.4733 kcal/mol        0.2119 kcal/(mol*A)
    xmin    30     -532.1218 kcal/mol        0.2393 kcal/(mol*A)
    xmin    40     -532.3906 kcal/mol        0.1166 kcal/(mol*A)
    xmin    50     -532.5734 kcal/mol        0.0668 kcal/(mol*A)
    xmin    60     -532.6690 kcal/mol        0.1177 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 GLC+GLC  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue GLC+GLC  
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 31.0.101.2111
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G3
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,054,666,752
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
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
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    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
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    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
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    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
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    Pygments: 2.16.1
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    PyOpenGL-accelerate: 3.1.7
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    PyQt6-Qt6: 6.3.2
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    PyQt6-WebEngine-Qt6: 6.3.2
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    requests: 2.31.0
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
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    typing-extensions: 4.9.0
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    wcwidth: 0.2.13
    webcolors: 1.12
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    wheel-filename: 1.4.1
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    WMI: 1.5.1