Add Charge failure

[johnfranciscortez.jfc@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Failure running ANTECHAMBER for residue UNL

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "C:\Users\johnf\Desktop\Academics\Bioinformatics\Ganoderma_Paper\Ligand_Files\SDF_Format\HMDB0032837
> (Ganoderic acid DM).sdf" format sdf

> dockprep

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to HMDB0032837 (Ganoderic acid
DM).sdf #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  
29 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.8/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\johnf\AppData\Local\Temp\tmpr98g2iik\ante.in.mol2 -fi mol2 -o
C:\Users\johnf\AppData\Local\Temp\tmpr98g2iik\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -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\johnf\AppData\Local\Temp\tmpr98g2iik\ante.in.mol2); atoms read (63),
bonds read (66).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX 1.8/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 1.8/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: 242; net charge: -1`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX 1.8/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(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 = 87
    
    | 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 =      165
    | QMMM:    diag iterations used for timing =        5
    | QMMM:
    | QMMM:              Internal diag routine = 0.063975 seconds
    | QMMM:                 Dspev diag routine = 0.053957 seconds
    | QMMM:                Dspevd diag routine = 0.042807 seconds
    | QMMM:                Dspevx diag routine = 0.191501 seconds
    | QMMM:                 Dsyev diag routine = 0.061198 seconds
    | QMMM:                Dsyevd diag routine = 0.050449 seconds
    | QMMM:                Dsyevr diag routine = 0.050166 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.031799 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        1.0300   -1.7900    0.0000
      QMMM:     2        2      C        0.6390   -4.6220    0.0000
      QMMM:     3        3      C        6.4230    0.8530    0.0000
      QMMM:     4        4      C        7.4210    0.4920    0.0000
      QMMM:     5        5      C        5.3340   -1.6190    0.0000
      QMMM:     6        6      C        2.8180   -2.0210    0.0000
      QMMM:     7        7      C        3.6560    0.2980    0.0000
      QMMM:     8        8      C        1.6520   -3.3190    0.0000
      QMMM:     9        9      C        2.1580   -2.6670    0.0000
      QMMM:    10       10      C        1.9630   -4.0830    0.0000
      QMMM:    11       11      C        2.1240   -0.4600    0.0000
      QMMM:    12       12      C        4.5220   -1.7640    0.0000
      QMMM:    13       13      C        6.9590   -1.3290    0.0000
      QMMM:    14       14      C        6.1460   -1.4740    0.0000
      QMMM:    15       15      C        3.7100   -1.9090    0.0000
      QMMM:    16       16      C        2.8070    0.0040    0.0000
      QMMM:    17       17      C        5.3630    0.5640    0.0000
      QMMM:    18       18      C        1.8470   -1.9030    0.0000
      QMMM:    19       19      C        1.4560   -4.7340    0.0000
      QMMM:    20       20      C        2.3540   -1.2520    0.0000
      QMMM:    21       21      C        4.8030   -0.9880    0.0000
      QMMM:    22       22      C        4.5510    0.4180    0.0000
      QMMM:    23       23      C        5.8950   -0.0670    0.0000
      QMMM:    24       24      C        7.2390   -0.5530    0.0000
      QMMM:    25       25      C        4.2710   -0.3580    0.0000
      QMMM:    26       26      C        1.7670   -5.4980    0.0000
      QMMM:    27       27      C        6.7070    0.0780    0.0000
      QMMM:    28       28      C        5.6150   -0.8430    0.0000
      QMMM:    29       29      C        3.1780   -1.2790    0.0000
      QMMM:    30       30      C        3.4590   -0.5030    0.0000
      QMMM:    31       31      O        4.0190    1.0490    0.0000
      QMMM:    32       32      O        8.0510   -0.4070    0.0000
      QMMM:    33       33      O        2.5850   -5.6110    0.0000
      QMMM:    34       34      O        1.2610   -6.1500    0.0000
      QMMM:    35       35      H        0.5820   -3.1710    0.0000
      QMMM:    36       36      H        3.2280   -2.8150    0.0000
      QMMM:    37       37      H        3.0330   -4.2310    0.0000
      QMMM:    38       38      H        1.1090   -0.0930    0.0000
      QMMM:    39       39      H        5.2180   -2.5900    0.0000
      QMMM:    40       40      H        7.6550   -2.1540    0.0000
      QMMM:    41       41      H        5.7790   -2.4900    0.0000
      QMMM:    42       42      H        3.3430   -2.9250    0.0000
      QMMM:    43       43      H        2.8420    1.0830    0.0000
      QMMM:    44       44      H        5.7300    1.5790    0.0000
      QMMM:    45       45      H        0.3670   -2.6430    0.0000
      QMMM:    46       46      H        0.6230   -0.7900    0.0000
      QMMM:    47       47      H        0.2320   -3.6210    0.0000
      QMMM:    48       48      H       -0.0240   -5.4740    0.0000
      QMMM:    49       49      H        7.2630    1.5480    0.0000
      QMMM:    50       50      H        5.8160    1.0160   -0.8900
      QMMM:    51       51      H        5.8150    1.0170    0.8900
      QMMM:    52       52      H        7.2190    1.5630    0.0000
      QMMM:    53       53      H        7.9920    0.2300   -0.8900
      QMMM:    54       54      H        7.9930    0.2300    0.8900
      QMMM:    55       55      H        6.1770   -2.3100    0.0000
      QMMM:    56       56      H        4.7280   -1.7860    0.8900
      QMMM:    57       57      H        4.7270   -1.7860   -0.8900
      QMMM:    58       58      H        3.5840   -2.7970    0.0000
      QMMM:    59       59      H        2.1980   -2.1240    0.8900
      QMMM:    60       60      H        2.1970   -2.1240   -0.8900
      QMMM:    61       61      H        2.7460    0.8970    0.0000
      QMMM:    62       62      H        4.2420    0.5280    0.8900
    

  
Failure running ANTECHAMBER for residue UNL  
Check reply log for details  




OpenGL version: 3.3.0 Core Profile Context 23.19.12.03.240603
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_PH.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82KT
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 6,280,699,904
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 3 5300U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
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File attachment: Report Log.txt

Report Log.txt​

[johnfranciscortez.jfc@…]

Added by email2trac

[pett]

Hi John,

Thanks for reporting this problem. When I open the structure for Ganoderic acid ("open pubchem:471002") I am able to add charges to it without problem, so I may need access to your HMDB0032837 (Ganoderic acid DM).sdf file to figure out what's going on. Also, I don't see any actual error message in the sqm output, which is weird. In the interim, you could try using Gasteiger charges instead of AM1-BCC in the Add Charge dialog, which would probably work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab