Opened 12 months ago

Last modified 12 months ago

#16279 feedback defect

Add Charge failure

Reported by: johnfranciscortez.jfc@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1
File attachment: Report Log.txt

Report Log.txt​

Attachments (1)

Report Log.txt​ (7.7 KB ) - added by johnfranciscortez.jfc@… 12 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by johnfranciscortez.jfc@…, 12 months ago

Attachment: Report Log.txt​ added

Added by email2trac

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Add Charge failure

comment:2 by Eric Pettersen, 12 months ago

Status: accepted → feedback

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

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