Add Charge failure

[chimerax-bug-report@…]

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)

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 D:/desi/18fdu1ivo.pdb

Summary of feedback from opening D:/desi/18fdu1ivo.pdb  
---  
warning | Ignored bad PDB record found on line 21846  
MASTER 0 0 0 0 0 0 0 0 10921 0 10921 0  
  
Chain information for 18fdu1ivo.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  

> close session

> open D:/desi/LIG.mol2

Opened LIG.mol2 containing 1 structure (218 atoms, 187 bonds)  

> 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 LIG.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:  
2 hydrogen bonds  
109 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 UNL+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\CHINMA~1\AppData\Local\Temp\tmpyasv0s9l\ante.in.mol2 -fi mol2 -o
C:\Users\CHINMA~1\AppData\Local\Temp\tmpyasv0s9l\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNL+UNL) ``  
(UNL+UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL+UNL) ``  
(UNL+UNL) `Info: Finished reading file
(C:\Users\CHINMA~1\AppData\Local\Temp\tmpyasv0s9l\ante.in.mol2); atoms read
(56), bonds read (57).`  
(UNL+UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL+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+UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL+UNL) ``  
(UNL+UNL) ``  
(UNL+UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL+UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL+UNL) `Info: Total number of electrons: 218; net charge: 0`  
(UNL+UNL) ``  
(UNL+UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNL+UNL) `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 = 81
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : 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 =      140
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.047207 seconds
    | QMMM:                 Dspev diag routine = 0.038821 seconds
    | QMMM:                Dspevd diag routine = 0.036781 seconds
    | QMMM:                Dspevx diag routine = 0.181602 seconds
    | QMMM:                 Dsyev diag routine = 0.045038 seconds
    | QMMM:                Dsyevd diag routine = 0.039038 seconds
    | QMMM:                Dsyevr diag routine = 0.050461 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.025719 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      136.9750   58.0000   47.6160
      QMMM:     2        2      C      137.7110   59.0230   46.7420
      QMMM:     3        3      C      137.4570   60.4830   47.1800
      QMMM:     4        4      C      136.0660   60.7630   47.8010
      QMMM:     5        5      C      135.5150   59.5730   48.5930
      QMMM:     6        6      C      134.0510   59.7360   48.9840
      QMMM:     7        7      C      139.8770   58.6470   45.7210
      QMMM:     8        8      C      140.1510   57.2450   45.2020
      QMMM:     9        9      N      139.1380   58.7590   46.8220
      QMMM:    10       10      H      139.5800   58.6580   47.7360
      QMMM:    11       11      O      137.6120   61.3240   46.0460
      QMMM:    12       12      H      137.4560   62.2220   46.3150
      QMMM:    13       13      O      136.1670   61.8850   48.7030
      QMMM:    14       14      O      135.6150   58.3820   47.8050
      QMMM:    15       15      O      133.8730   59.6680   50.3950
      QMMM:    16       16      H      132.9600   59.7700   50.6390
      QMMM:    17       17      O      140.3500   59.6180   45.1300
      QMMM:    18       18      C      136.2510   63.1800   48.2020
      QMMM:    19       19      C      134.9680   63.5300   47.4150
      QMMM:    20       20      C      134.8930   65.0350   47.0940
      QMMM:    21       21      C      135.1880   65.8910   48.3330
      QMMM:    22       22      C      136.4860   65.4360   49.0020
      QMMM:    23       23      C      136.7540   66.1820   50.2970
      QMMM:    24       24      C      133.8690   62.7740   45.3940
      QMMM:    25       25      C      134.0090   63.4100   44.0160
      QMMM:    26       26      N      134.9450   62.7680   46.1770
      QMMM:    27       27      H      135.7630   62.2230   45.9050
      QMMM:    28       28      O      133.5930   65.3510   46.6090
      QMMM:    29       29      H      133.5470   66.2790   46.4110
      QMMM:    30       30      O      135.3020   67.2560   47.9550
      QMMM:    31       31      H      135.4850   67.7860   48.7220
      QMMM:    32       32      O      136.3990   64.0400   49.3420
      QMMM:    33       33      O      136.3520   65.4160   51.4270
      QMMM:    34       34      H      136.5200   65.8830   52.2370
      QMMM:    35       35      O      132.7910   62.2900   45.7400
      QMMM:    36       36      H      137.0080   57.0250   47.1300
      QMMM:    37       37      H      137.4680   57.9350   48.5860
      QMMM:    38       38      H      137.3870   58.9030   45.7080
      QMMM:    39       39      H      138.2170   60.7560   47.9120
      QMMM:    40       40      H      135.3660   61.0120   47.0040
      QMMM:    41       41      H      136.1090   59.4470   49.4980
      QMMM:    42       42      H      133.6960   60.7040   48.6290
      QMMM:    43       43      H      133.4660   58.9470   48.5120
      QMMM:    44       44      H      137.1220   63.2710   47.5530
      QMMM:    45       45      H      134.1010   63.2540   48.0150
      QMMM:    46       46      H      135.6250   65.2680   46.3210
      QMMM:    47       47      H      134.3670   65.7860   49.0420
      QMMM:    48       48      H      137.3200   65.5900   48.3170
      QMMM:    49       49      H      137.8210   66.3920   50.3720
      QMMM:    50       50      H      136.2040   67.1230   50.2880
      QMMM:    51       51      H      140.7630   57.3030   44.3020
      QMMM:    52       52      H      140.6790   56.6720   45.9640
      QMMM:    53       53      H      139.2070   56.7530   44.9680
      QMMM:    54       54      H      133.0580   63.3450   43.4870
      QMMM:    55       55      H      134.2920   64.4570   44.1260
      QMMM:    56       56      H      134.7770   62.8830   43.4490
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10     -431.0602 kcal/mol        1.4750 kcal/(mol*A)
    xmin    20     -447.2166 kcal/mol        0.9682 kcal/(mol*A)
    xmin    30     -452.0095 kcal/mol        1.2312 kcal/(mol*A)
    xmin    40     -453.3883 kcal/mol        0.3131 kcal/(mol*A)
    xmin    50     -454.1349 kcal/mol        0.1531 kcal/(mol*A)
    xmin    60     -454.7102 kcal/mol        0.1969 kcal/(mol*A)
    xmin    70     -455.6063 kcal/mol        0.2513 kcal/(mol*A)
    xmin    80     -456.2876 kcal/mol        0.1950 kcal/(mol*A)
    xmin    90     -457.5416 kcal/mol        0.7670 kcal/(mol*A)
    xmin   100     -457.9727 kcal/mol        0.1087 kcal/(mol*A)
    xmin   110     -458.7870 kcal/mol        0.5095 kcal/(mol*A)
    xmin   120     -459.4025 kcal/mol        0.0740 kcal/(mol*A)
    xmin   130     -459.4978 kcal/mol        0.0489 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 UNL+UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL+UNL  
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:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
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