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#9566 closed defect (limitation)
Antechamber failure
| Reported by: | 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
Attachments (1)
Change History (5)
by , 2 years ago
| Attachment: | 1qs0_couloumbic.log added |
|---|
comment:1 by , 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: ------------------------+----------------------------- -- Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f9566&umid=1A57EC47-02BC-AA06-B99E-CA1684191E3A&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-f0870a33c00e07de7d1627cf08d35b118177221c> ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=1A57EC47-02BC-AA06-B99E-CA1684191E3A&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-2682dbf4e700b8b33e139b76e9f3cc86cf5a4381> ChimeraX Issue Tracker
comment:2 by , 2 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Antechamber failure |
comment:3 by , 2 years ago
| Cc: | added |
|---|---|
| Resolution: | → limitation |
| Status: | accepted → closed |
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 , 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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