sqm failure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
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
> D:\OneDrive\PhD\CIAD\Materias\2024-1-Tesis_III\Molecules_Charmm\Substrates\ATP\Docked_ATP_3.1_mod.mol2
> format mol2

Opened Docked_ATP_3.1_mod.mol2 containing 1 structure (39 atoms, 41 bonds)  

> select add #1

39 atoms, 41 bonds, 1 residue, 1 model selected  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  

> rename #1 ATP.mol2

> 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 ATP.mol2 #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  
8 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 -4) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\Felix\AppData\Local\Temp\tmpex_vaf3s\ante.in.mol2 -fi mol2 -o
C:\Users\Felix\AppData\Local\Temp\tmpex_vaf3s\ante.out.mol2 -fo mol2 -c bcc
-nc -4 -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\Felix\AppData\Local\Temp\tmpex_vaf3s\ante.in.mol2); atoms read (47),
bonds read (49).`  
(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: 264; net charge: -4`  
(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 = 89
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: C : 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: N : 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 = 0.029179 seconds
    | QMMM:                 Dspev diag routine = 0.023125 seconds
    | QMMM:                Dspevd diag routine = 0.018445 seconds
    | QMMM:                Dspevx diag routine = 0.092941 seconds
    | QMMM:                 Dsyev diag routine = 0.025612 seconds
    | QMMM:                Dsyevd diag routine = 0.021658 seconds
    | QMMM:                Dsyevr diag routine = 0.023769 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.010576 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      O       19.2830    5.9790   16.9630
      QMMM:     2        2      C       17.9260    7.5360   18.1220
      QMMM:     3        3      C       17.1280    6.2600   17.9350
      QMMM:     4        4      C       19.3500    7.0310   17.9450
      QMMM:     5        5      C       17.9080    5.5480   16.8360
      QMMM:     6        6      C       17.4210    5.9020   15.4370
      QMMM:     7        7      O       18.4060    5.5180   14.4940
      QMMM:     8        8      P       18.1650    5.7900   12.9170
      QMMM:     9        9      O       19.4170    6.0020   12.1160
      QMMM:    10       10      O       17.2670    4.5430   12.4220
      QMMM:    11       11      P       15.7580    4.4730   11.8500
      QMMM:    12       12      O       15.3320    3.1300   11.3330
      QMMM:    13       13      O       15.7180    5.6600   10.7550
      QMMM:    14       14      P       15.6460    5.6340    9.1410
      QMMM:    15       15      O       16.1680    6.8710    8.4720
      QMMM:    16       16      O       16.4230    4.2690    8.7610
      QMMM:    17       17      H       15.9030    3.4940    8.4580
      QMMM:    18       18      O       14.0980    5.2840    8.8360
      QMMM:    19       19      H       13.4330    5.4100    9.5470
      QMMM:    20       20      O       14.8590    5.0490   13.0630
      QMMM:    21       21      H       15.1250    5.8880   13.4970
      QMMM:    22       22      O       17.1300    7.0310   12.8770
      QMMM:    23       23      H       16.8550    7.3930   12.0070
      QMMM:    24       24      O       17.1950    5.4780   19.1280
      QMMM:    25       25      H       16.2840    5.3710   19.4530
      QMMM:    26       26      N       20.2950    8.0550   17.5060
      QMMM:    27       27      C       21.3150    8.6000   18.2360
      QMMM:    28       28      N       21.6600    8.3100   19.5000
      QMMM:    29       29      C       21.9190    9.5170   17.3900
      QMMM:    30       30      C       22.7210    9.0540   19.8800
      QMMM:    31       31      N       23.4070    9.9820   19.1710
      QMMM:    32       32      C       23.0030   10.2230   17.9010
      QMMM:    33       33      N       21.2910    9.5400   16.1700
      QMMM:    34       34      C       20.3240    8.6520   16.2720
      QMMM:    35       35      N       23.6750   11.1740   17.1130
      QMMM:    36       36      H       24.0190   10.9260   16.1950
      QMMM:    37       37      H       23.8100   12.1080   17.4760
      QMMM:    38       38      O       17.7320    8.1300   19.3900
      QMMM:    39       39      H       17.0340    8.8020   19.3090
      QMMM:    40       40      H       17.6810    8.2480   17.3340
      QMMM:    41       41      H       16.0990    6.4630   17.6380
      QMMM:    42       42      H       19.6970    6.6120   18.8900
      QMMM:    43       43      H       17.8470    4.4700   16.9830
      QMMM:    44       44      H       16.4910    5.3730   15.2290
      QMMM:    45       45      H       17.2520    6.9770   15.3710
      QMMM:    46       46      H       23.0710    8.8860   20.8880
      QMMM:    47       47      H       19.6330    8.4210   15.4750
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10     -506.9822 kcal/mol        5.9784 kcal/(mol*A)
    xmin    20     -542.6041 kcal/mol        2.9860 kcal/(mol*A)
    xmin    30     -554.8419 kcal/mol        2.7063 kcal/(mol*A)
    xmin    40     -560.2556 kcal/mol        1.4779 kcal/(mol*A)
    xmin    50     -565.3064 kcal/mol        1.6178 kcal/(mol*A)
    xmin    60     -568.0964 kcal/mol        0.7597 kcal/(mol*A)
    xmin    70     -569.5396 kcal/mol        1.4394 kcal/(mol*A)
    xmin    80     -570.6783 kcal/mol        1.6108 kcal/(mol*A)
    xmin    90     -571.3600 kcal/mol        0.5723 kcal/(mol*A)
    xmin   100     -571.7512 kcal/mol        0.2441 kcal/(mol*A)
    xmin   110     -571.8727 kcal/mol        0.2373 kcal/(mol*A)
    xmin   120     -572.0318 kcal/mol        0.7963 kcal/(mol*A)
    xmin   130     -572.2925 kcal/mol        0.9376 kcal/(mol*A)
    xmin   140     -572.5659 kcal/mol        0.5014 kcal/(mol*A)
    xmin   150     -572.7989 kcal/mol        0.6307 kcal/(mol*A)
    xmin   160     -573.2042 kcal/mol        0.4810 kcal/(mol*A)
    xmin   170     -573.4645 kcal/mol        0.5981 kcal/(mol*A)
    xmin   180     -573.5873 kcal/mol        0.2131 kcal/(mol*A)
    xmin   190     -573.6915 kcal/mol        0.2891 kcal/(mol*A)
    xmin   200     -573.8590 kcal/mol        0.2611 kcal/(mol*A)
    xmin   210     -573.9898 kcal/mol        0.4327 kcal/(mol*A)
    xmin   220     -574.1111 kcal/mol        0.0920 kcal/(mol*A)
    xmin   230     -574.1891 kcal/mol        0.6010 kcal/(mol*A)
    xmin   240     -574.2403 kcal/mol        0.4391 kcal/(mol*A)
    xmin   250     -574.3269 kcal/mol        0.1190 kcal/(mol*A)
    xmin   260     -574.4616 kcal/mol        0.3498 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 NVIDIA 551.61
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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: Micro-Star International Co., Ltd.
Model: MS-7C95
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 17,102,323,712
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800X 8-Core Processor             
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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    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

[Eric Pettersen]

sqm was not rerun because "No convergence in SCF" was not in the output. Probably would have worked if the residue name was ATP instead of UNK.