id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14813 Antechamber failure mayacheung@… Eric Pettersen "{{{ 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 I am trying to prep a ligand for docking but when there is a failure running ANTECHAMBER for residue UNL. This has happened to be multiple times and I am not sure what to do. I have prepped a different ligand before and it worked fine so I am not sure why it is not working now. Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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/mayac/OneDrive/Desktop/250 Project/compound9_ligand.mol"" > 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 compound9_ligand.mol #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 20 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 UNL (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\mayac\AppData\Local\Temp\tmpj416qjnp\ante.in.mol2 -fi mol2 -o C:\Users\mayac\AppData\Local\Temp\tmpj416qjnp\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\mayac\AppData\Local\Temp\tmpj416qjnp\ante.in.mol2); atoms read (44), bonds read (46).` (UNL) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNL) `Running: ""C:/Program Files/ChimeraX/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/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: 182; net charge: 1` (UNL) `` (UNL) `Running: ""C:/Program Files/ChimeraX/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 = 63 | 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: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988) | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990) | 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 = 116 | QMMM: diag iterations used for timing = 10 | QMMM: | QMMM: Internal diag routine = 0.065801 seconds | QMMM: Dspev diag routine = 0.035281 seconds | QMMM: Dspevd diag routine = 0.024201 seconds | QMMM: Dspevx diag routine = 0.128448 seconds | QMMM: Dsyev diag routine = 0.052337 seconds | QMMM: Dsyevd diag routine = 0.039069 seconds | QMMM: Dsyevr diag routine = 0.036476 seconds | QMMM: | QMMM: Pseudo diag routine = 0.013025 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 2.6180 1.5330 -4.4630 QMMM: 2 2 C 2.2650 2.8020 -4.9630 QMMM: 3 3 C 1.1660 3.4920 -4.4190 QMMM: 4 4 C 0.4070 2.9070 -3.3910 QMMM: 5 5 C 0.7590 1.6400 -2.8860 QMMM: 6 6 C 1.8790 0.9410 -3.4120 QMMM: 7 7 C 2.2040 -0.3170 -2.8480 QMMM: 8 8 N 0.0350 1.0980 -1.8740 QMMM: 9 9 C 0.3590 -0.0810 -1.2770 QMMM: 10 10 C 1.4480 -0.8290 -1.7750 QMMM: 11 11 F 2.9580 3.3390 -5.9320 QMMM: 12 12 O 3.1730 -0.9900 -3.2700 QMMM: 13 13 C -0.4030 -0.4810 -0.0700 QMMM: 14 14 N 0.2250 0.0060 1.1830 QMMM: 15 15 C 0.3370 1.4810 1.3040 QMMM: 16 16 C 0.8420 1.9580 2.6960 QMMM: 17 17 C -0.0480 1.4720 3.8890 QMMM: 18 18 C -1.4460 1.9760 3.8540 QMMM: 19 19 S -3.9370 2.2710 3.3480 QMMM: 20 20 C -2.4910 1.2860 3.2210 QMMM: 21 21 C -1.8420 3.2040 4.4340 QMMM: 22 22 C -3.1830 3.5590 4.2660 QMMM: 23 23 C 1.0330 3.5070 2.6780 QMMM: 24 24 O 1.5250 3.9950 3.9230 QMMM: 25 25 H 3.4610 1.0070 -4.8870 QMMM: 26 26 H 0.9060 4.4720 -4.7920 QMMM: 27 27 H -0.4470 3.4300 -2.9870 QMMM: 28 28 H -0.7830 1.5930 -1.5480 QMMM: 29 29 H 1.6980 -1.7840 -1.3380 QMMM: 30 30 H -1.4100 -0.0690 -0.1400 QMMM: 31 31 H -0.4670 -1.5690 -0.0360 QMMM: 32 32 H -0.3270 -0.3300 1.9590 QMMM: 33 33 H 1.1500 -0.3920 1.2520 QMMM: 34 34 H 1.0330 1.8370 0.5440 QMMM: 35 35 H -0.6420 1.9230 1.1160 QMMM: 36 36 H 1.8300 1.5200 2.8410 QMMM: 37 37 H 0.4130 1.8070 4.8180 QMMM: 38 38 H -0.0700 0.3820 3.8850 QMMM: 39 39 H -2.4180 0.3220 2.7410 QMMM: 40 40 H -1.1490 3.8300 4.9760 QMMM: 41 41 H -3.6630 4.4560 4.6310 QMMM: 42 42 H 1.7440 3.7650 1.8920 QMMM: 43 43 H 0.0760 3.9810 2.4620 QMMM: 44 44 H 1.6300 4.9480 3.8740 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- iter sqm energy rms gradient ---- ------------------- ----------------------- xmin 10 91.3357 kcal/mol 1.5593 kcal/(mol*A) xmin 20 90.7656 kcal/mol 0.2814 kcal/(mol*A) xmin 30 90.6410 kcal/mol 0.3855 kcal/(mol*A) xmin 40 90.4602 kcal/mol 0.8736 kcal/(mol*A) xmin 50 90.2729 kcal/mol 0.2639 kcal/(mol*A) xmin 60 90.1241 kcal/mol 0.2699 kcal/(mol*A) xmin 70 90.0355 kcal/mol 0.3978 kcal/(mol*A) xmin 80 89.9055 kcal/mol 0.3962 kcal/(mol*A) xmin 90 89.8435 kcal/mol 0.1990 kcal/(mol*A) xmin 100 89.7675 kcal/mol 0.3981 kcal/(mol*A) xmin 110 89.6974 kcal/mol 0.3630 kcal/(mol*A) xmin 120 89.6197 kcal/mol 0.3766 kcal/(mol*A) xmin 130 89.4753 kcal/mol 0.5124 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 UNL Check reply log for details chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for residue UNL 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: 3.3.0 - Build 30.0.100.9805 OpenGL renderer: Intel(R) Iris(R) Plus Graphics OpenGL vendor: Intel Python: 3.11.2 Locale: en_CA.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Acer Model: Spin SP314-54N OS: Microsoft Windows 11 Home (Build 22631) Memory: 8,367,693,824 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-1035G4 CPU @ 1.10GHz OSLanguage: en-US 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 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 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 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 File attachment: compound9_ligand.mol }}} [attachment:""compound9_ligand.mol""] " defect closed normal Structure Editing can't reproduce all ChimeraX