Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9566 closed defect (limitation)

Antechamber failure

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

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-155-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.dev202307130149 (2023-07-13 01:49:10 UTC)
Description
Hi,
I'm trying to reproduce coulomb surface coloring accrordint to example sent by Elaine on 1qs0:
open 1qs0
surf include :tpp
coulombic surfaces #1.2
 
But  I get an error about failure (see logfile included) to do with runningn Antechamber.

The program suggests to look in the reply.log but I'm not sure where to look for it in Chimerax. I therefore pasted the report from the log on the screen into the attached file.


Log:
UCSF ChimeraX version: 1.7.dev202307130149 (2023-07-13)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/boaz/chimera_models/1qs0.pdb format pdb

1qs0.pdb title:  
Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase
(branched-chain α-keto acid dehydrogenase, E1B) [more info...]  
  
Chain information for 1qs0.pdb #1  
---  
Chain | Description | UniProt  
A | 2-oxoisovalerate dehydrogenase α-subunit | ODBA_PSEPU 2-408  
B | 2-oxoisovalerate dehydrogenase β-subunit | ODBB_PSEPU 2-339  
  
Non-standard residues in 1qs0.pdb #1  
---  
COI — 2-oxo-4-methylpentanoic acid (α-ketoisocaproic acid)  
MG — magnesium ion  
TPP — thiamine diphosphate  
  

> surface include :tpp

> coulombic surfaces #1.2

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue TPP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmprxr5rh03/ante.in.mol2 -fi mol2 -o /tmp/tmprxr5rh03/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(TPP) ``  
(TPP) `Welcome to antechamber 20.0: molecular input file processor.`  
(TPP) ``  
(TPP) `Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read
(42), bonds read (43).`  
(TPP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TPP) ``  
(TPP) ``  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TPP) `Info: Total number of electrons: 220; net charge: -2`  
(TPP) ``  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`  
(TPP) `/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error!`  
(TPP) `Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmprxr5rh03/ante.in.mol2 -fi mol2 -o
/tmp/tmprxr5rh03/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(TPP) ``  
(TPP) `Welcome to antechamber 20.0: molecular input file processor.`  
(TPP) ``  
(TPP) `Info: Finished reading file (/tmp/tmprxr5rh03/ante.in.mol2); atoms read
(42), bonds read (43).`  
(TPP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TPP) ``  
(TPP) ``  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TPP) `Info: Total number of electrons: 220; net charge: -2`  
(TPP) ``  
(TPP) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`  
(TPP) `/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error!`  
(TPP) `Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out".`  
  
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 = 72
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
    | QMMM: O : 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: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | 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 =      120
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.046243 seconds
    | QMMM:                 Dspev diag routine = 0.024207 seconds
    | QMMM:                Dspevd diag routine = 0.017766 seconds
    | QMMM:                Dspevx diag routine = 0.090484 seconds
    | QMMM:                 Dsyev diag routine = 0.026991 seconds
    | QMMM:                Dsyevd diag routine = 0.020813 seconds
    | QMMM:                Dsyevr diag routine = 0.023803 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.010291 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      N       -6.5270   -9.5340  108.8420
      QMMM:     2        2      C       -5.1860   -9.8350  109.0420
      QMMM:     3        3      C       -4.1430   -8.7560  109.0940
      QMMM:     4        4      N       -4.7780  -11.0890  109.1960
      QMMM:     5        5      C       -5.6960  -12.1350  109.1610
      QMMM:     6        6      N       -5.1880  -13.3540  109.3240
      QMMM:     7        7      C       -7.1000  -11.8740  108.9590
      QMMM:     8        8      C       -7.4370  -10.5640  108.8080
      QMMM:     9        9      C       -8.1400  -12.9880  108.9090
      QMMM:    10       10      N       -7.9780  -13.7930  107.6090
      QMMM:    11       11      C       -7.2960  -14.9300  107.6450
      QMMM:    12       12      S       -7.1510  -15.7280  106.1910
      QMMM:    13       13      C       -8.0580  -14.4980  105.4120
      QMMM:    14       14      C       -8.4380  -13.5160  106.3190
      QMMM:    15       15      C       -9.2300  -12.3130  105.9590
      QMMM:    16       16      C       -8.3050  -14.6150  103.9530
      QMMM:    17       17      C       -7.1840  -14.0870  103.0870
      QMMM:    18       18      O       -7.2870  -14.5610  101.7840
      QMMM:    19       19      P       -6.2950  -14.6650  100.5520
      QMMM:    20       20      O       -7.0190  -14.6260   99.2930
      QMMM:    21       21      O       -5.2170  -13.6750  100.7960
      QMMM:    22       22      O       -5.6780  -16.0660  100.8100
      QMMM:    23       23      P       -6.2660  -17.5600  100.7830
      QMMM:    24       24      O       -7.2020  -17.5030   99.5940
      QMMM:    25       25      O       -5.0830  -18.4600  100.4010
      QMMM:    26       26      O       -7.0330  -17.7290  102.0100
      QMMM:    27       27      H       -8.4780  -10.3200  108.6530
      QMMM:    28       28      H       -9.1390  -12.5530  108.9430
      QMMM:    29       29      H       -8.0040  -13.6500  109.7640
      QMMM:    30       30      H       -6.8630  -15.3130  108.5570
      QMMM:    31       31      H       -8.4520  -15.6690  103.7150
      QMMM:    32       32      H       -9.2180  -14.0720  103.7100
      QMMM:    33       33      H       -6.2300  -14.4070  103.5070
      QMMM:    34       34      H       -7.2230  -12.9980  103.0760
      QMMM:    35       35      H       -4.2060  -13.1240  109.3710
      QMMM:    36       36      H       -5.6510  -14.2500  109.3830
      QMMM:    37       37      H       -4.0080   -8.3320  108.0990
      QMMM:    38       38      H       -4.4640   -7.9740  109.7820
      QMMM:    39       39      H       -3.2000   -9.1790  109.4400
      QMMM:    40       40      H       -9.3950  -11.7060  106.8490
      QMMM:    41       41      H       -8.6860  -11.7290  105.2170
      QMMM:    42       42      H      -10.1910  -12.6210  105.5460
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.8342E+06 DeltaE =  -0.8519E-02 DeltaP =   0.2665E-02
    QMMM: Smallest DeltaE =   0.8221E-05 DeltaP =   0.1967E-02 Step =    292
    
    

  
Failure running ANTECHAMBER for residue TPP  
Check reply log for details  

> select add #1

5999 atoms, 5942 bonds, 7 pseudobonds, 945 residues, 2 models selected  

> select subtract #1

2 models selected  

> view

> help help:user

[Repeated 1 time(s)]

> help help:user/preferences.html#startup

[Repeated 1 time(s)]




OpenGL version: 3.3.0 NVIDIA 470.199.02
OpenGL renderer: Quadro T2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 5540
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9850H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       2.8Gi        10Gi       102Mi       2.4Gi        12Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Mobile) [8086:3e9b] (rev 02)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell UHD Graphics 630 (Mobile) [1028:0906]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    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: 2.10.4
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307130149
    ChimeraX-CoreFormats: 1.1
    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: 1.1.2
    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: 1.2.1
    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: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    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: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 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: 1.30.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    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: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
File attachment: 1qs0_couloumbic.log

1qs0_couloumbic.log

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1qs0_couloumbic.log (8.9 KB ) - added by bshaanan@… 2 years ago.
Added by email2trac

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Change History (5)

by bshaanan@…, 2 years ago

Attachment: 1qs0_couloumbic.log added

Added by email2trac

comment:1 by bshaanan@…, 2 years ago

Hi,
I made another attempt, adding another step to Elaine's protocol and it seems to have worked. This time there is a complaint about failure of the fast version of Antechamber and switching to the slow version, which apparently has worked. I am pasting the log window of the turn below.
I hope this info would be of help.
Cheers,
Boaz


UCSF ChimeraX version: 1.7.dev202307130149 (2023-07-13)
© 2016-2023 Regents of the University of California. All rights reserved.

open /home/boaz/chimera_models/1qs0_1.cxs format session
Log from Sun Aug 13 19:42:57 2023






<http://www.rcsb.org/ligand/COI>
<http://www.rcsb.org/ligand/MG>
<http://www.rcsb.org/ligand/TPP>














































































opened ChimeraX session

~select
Nothing selected

coulombic surfaces #1.2
Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue TPP (net charge -2) with am1-bcc method
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp9oxvwqvw/ante.in.mol2 -fi mol2 -o /tmp/tmp9oxvwqvw/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(TPP)
(TPP) Welcome to antechamber 20.0: molecular input file processor.
(TPP)
(TPP) Info: Finished reading file (/tmp/tmp9oxvwqvw/ante.in.mol2); atoms read (42), bonds read (43).
(TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(TPP)
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(TPP) Info: Total number of electrons: 220; net charge: -2
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(TPP) /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber: Fatal Error!
(TPP) Cannot properly run "/usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out".
Charges failed to converge using fast method; re-running using slower more stable method
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -i /tmp/tmp9oxvwqvw/ante.in.mol2 -fi mol2 -o /tmp/tmp9oxvwqvw/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(TPP)
(TPP) Welcome to antechamber 20.0: molecular input file processor.
(TPP)
(TPP) Info: Finished reading file (/tmp/tmp9oxvwqvw/ante.in.mol2); atoms read (42), bonds read (43).
(TPP) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(TPP)
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(TPP) Info: Total number of electrons: 220; net charge: -2
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(TPP)
(TPP) Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(TPP)
Charges for residue TPP determined
Coulombic values for 1qs0.pdb_A SES surface #1.2: minimum, -18.77, mean -2.80, maximum 8.66

surface

surface include :tpp

coulombic surfaces #1.2
Coulombic values for 1qs0.pdb_A SES surface #1.2: minimum, -18.77, mean -2.80, maximum 8.66


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710




________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Saturday, August 12, 2023 12:53 PM
To: בעז שאנן <bshaanan@bgu.ac.il>
Subject: Re: [ChimeraX] #9566: ChimeraX bug report submission

#9566: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  bshaanan@…  |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
--
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comment:2 by Eric Pettersen, 2 years ago

Component: UnassignedStructure Editing
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionAntechamber failure

comment:3 by Eric Pettersen, 2 years ago

Cc: Elaine Meng added
Resolution: limitation
Status: acceptedclosed

Hi Boaz,

The calculation always works on my Mac (though it does have to fall back to the slower method). The sqm package that Antechamber uses undoubtedly has slightly different behavior on different platforms due to differences in floating-point formats, compiler types and options used to compile its numerical libraries, etc. Sqm in particular struggles with structures with areas of concentrated negative charge, such as TPP's phosphate chain.
We are investigating an alternative charge-determination method in OpenMM, but that is still early days.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:4 by bshaanan@…, 2 years ago

Thanks Eric for clarifying the point.
Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Aug 14, 2023 21:48, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#9566: Antechamber failure
----------------------------------------+--------------------
          Reporter:  bshaanan@…         |      Owner:  pett
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  limitation         |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+--------------------
Changes (by pett):

 * cc: Elaine Meng (added)
 * resolution:   => limitation
 * status:  accepted => closed

Comment:

 Hi Boaz,
         The calculation always works on my Mac (though it does have to
 fall back to the slower method).  The sqm package that Antechamber uses
 undoubtedly has slightly different behavior on different platforms due to
 differences in floating-point formats, compiler types and options used to
 compile its numerical libraries, etc.  Sqm in particular struggles with
 structures with areas of concentrated negative charge, such as TPP's
 phosphate chain.
         We are investigating an alternative charge-determination method in
 OpenMM, but that is still early days.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
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