Dock Prep ChargeError

[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  
---  
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\Rajeev Abraham\OneDrive\Desktop\Simone\UBC\Courses\BMEG
> 250\Project\Final\Ligand.mol2" format mol2

No such file/path: C:\Users\Rajeev
Abraham\OneDrive\Desktop\Simone\UBC\Courses\BMEG 250\Project\Final\Ligand.mol2  

> open "C:\Users\Rajeev Abraham\OneDrive\Desktop\Simone\UBC\Courses\BMEG
> 250\Project\Final\Ligand.mol2" format mol2

No such file/path: C:\Users\Rajeev
Abraham\OneDrive\Desktop\Simone\UBC\Courses\BMEG 250\Project\Final\Ligand.mol2  

> open "C:/Users/Rajeev Abraham/OneDrive/Desktop/Simone/UBC/Courses/BMEG
> 250/Project/Final/Ligand - SKF-81297.mol2"

Opened Ligand - SKF-81297.mol2 containing 1 structure (36 atoms, 38 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 Ligand - SKF-81297.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:  
0 hydrogen bonds  
1 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 noname (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\RAJEEV~1\AppData\Local\Temp\tmpewd7670y\ante.in.mol2 -fi mol2 -o
C:\Users\RAJEEV~1\AppData\Local\Temp\tmpewd7670y\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(noname) ``  
(noname) `Welcome to antechamber 20.0: molecular input file processor.`  
(noname) ``  
(noname) `Info: Finished reading file
(C:\Users\RAJEEV~1\AppData\Local\Temp\tmpewd7670y\ante.in.mol2); atoms read
(37), bonds read (39).`  
(noname) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(noname) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(noname) `bash.exe: warning: could not find /tmp, please create!`  
(noname) ``  
(noname) ``  
(noname) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(noname) `bash.exe: warning: could not find /tmp, please create!`  
(noname) `Info: Total number of electrons: 152; net charge: 1`  
(noname) ``  
(noname) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(noname) `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 = 52
    
    | 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: Cl: M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | 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 =       97
    | QMMM:    diag iterations used for timing =       15
    | QMMM:
    | QMMM:              Internal diag routine = 0.047036 seconds
    | QMMM:                 Dspev diag routine = 0.051895 seconds
    | QMMM:                Dspevd diag routine = 0.044836 seconds
    | QMMM:                Dspevx diag routine = 0.151283 seconds
    | QMMM:                 Dsyev diag routine = 0.057644 seconds
    | QMMM:                Dsyevd diag routine = 0.056770 seconds
    | QMMM:                Dsyevr diag routine = 0.048778 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.018660 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        1.8820   -2.7350    1.0190
      QMMM:     2        2      C        0.9310   -2.9640    2.2150
      QMMM:     3        3      N       -0.0230   -1.8510    2.3720
      QMMM:     4        4      C       -1.0460   -1.7400    1.3150
      QMMM:     5        5      C       -0.5270   -1.2240   -0.0700
      QMMM:     6        6      C        0.1870   -2.3230   -0.8330
      QMMM:     7        7      C       -0.2620   -2.5950   -2.1490
      QMMM:     8        8      C        0.2920   -3.6250   -2.9210
      QMMM:     9        9      C        1.2930   -4.4430   -2.3770
      QMMM:    10       10      C        1.7980   -4.1760   -1.0850
      QMMM:    11       11      C        1.2810   -3.0890   -0.3110
      QMMM:    12       12      Cl       3.0410   -5.2040   -0.5370
      QMMM:    13       13      O        1.7480   -5.4720   -3.1470
      QMMM:    14       14      O       -0.1420   -3.8320   -4.1910
      QMMM:    15       15      C        0.1530    0.1240   -0.0430
      QMMM:    16       16      C        1.4230    0.3700   -0.6310
      QMMM:    17       17      C        1.9970    1.6550   -0.6340
      QMMM:    18       18      C        1.3030    2.7370   -0.0690
      QMMM:    19       19      C        0.0400    2.5300    0.5080
      QMMM:    20       20      C       -0.5220    1.2400    0.5210
      QMMM:    21       21      H        2.0670   -1.6620    0.9740
      QMMM:    22       22      H        2.7140   -3.4260    1.1520
      QMMM:    23       23      H        0.3220   -3.8360    1.9800
      QMMM:    24       24      H        1.5410   -2.9530    3.1180
      QMMM:    25       25      H        0.0220   -1.2080    3.1500
      QMMM:    26       26      H       -1.3860   -2.7640    1.1600
      QMMM:    27       27      H       -1.7390   -0.9860    1.6890
      QMMM:    28       28      H       -1.3770   -0.9660   -0.7000
      QMMM:    29       29      H       -1.0600   -1.9920   -2.5830
      QMMM:    30       30      H        2.0620   -6.1810   -2.5810
      QMMM:    31       31      H       -0.2000   -4.7750   -4.3600
      QMMM:    32       32      H        1.9720   -0.4500   -1.0930
      QMMM:    33       33      H        2.9810    1.8110   -1.0750
      QMMM:    34       34      H        1.7430    3.7350   -0.0780
      QMMM:    35       35      H       -0.5030    3.3680    0.9450
      QMMM:    36       36      H       -1.5020    1.1030    0.9780
      QMMM:    37       37      H        0.5910   -1.2500    1.8410
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10      103.2362 kcal/mol        6.4653 kcal/(mol*A)
    xmin    20      101.3008 kcal/mol        1.2150 kcal/(mol*A)
    xmin    30      100.6899 kcal/mol        0.5897 kcal/(mol*A)
    xmin    40      100.5273 kcal/mol        0.2609 kcal/(mol*A)
    xmin    50      100.4176 kcal/mol        1.0128 kcal/(mol*A)
    xmin    60      100.3605 kcal/mol        0.2694 kcal/(mol*A)
    xmin    70      100.3093 kcal/mol        0.4089 kcal/(mol*A)
    xmin    80      100.2670 kcal/mol        0.4265 kcal/(mol*A)
    xmin    90      100.2210 kcal/mol        0.4039 kcal/(mol*A)
    xmin   100      100.1922 kcal/mol        0.2703 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 noname  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue noname  
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: 3.3.14761 Core Profile Forward-Compatible Context 21.30.44 30.0.13044.0
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics
OpenGL vendor: ATI Technologies Inc.

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 Laptop 15s-eq0xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 6,355,144,704
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx  
OSLanguage: en-GB

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
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    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
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    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
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    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-PDBBio: 1.0.1
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    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
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    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
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    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
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    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
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    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
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    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1