id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9566 Antechamber failure bshaanan@… Eric Pettersen "{{{ 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 }}} [attachment:""1qs0_couloumbic.log""] " defect closed normal Structure Editing limitation Elaine Meng all ChimeraX