id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8576 ChargeError produces traceback chimerax-bug-report@… Eric Pettersen "The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open ""C:\Users\ricar\Downloads\Ejemplo DGE\Diabetes\Docking-EGFR\diana- min.pdb"" format pdb Summary of feedback from opening C:\Users\ricar\Downloads\Ejemplo DGE\Diabetes\Docking-EGFR\diana-min.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK File generated by Swiss-PdbViewer 4.00b0 Ignored bad PDB record found on line 2 REMARK http://www.expasy.org/spdbv/ Ignored bad PDB record found on line 4951 SPDBVT 1.0000000000 0.0000000000 0.0000000000 Ignored bad PDB record found on line 4952 SPDBVT 0.0000000000 1.0000000000 0.0000000000 Ignored bad PDB record found on line 4953 SPDBVT 0.0000000000 0.0000000000 1.0000000000 240 messages similar to the above omitted diana-min.pdb title: The egf-bound EGFR/HER2 ectodomain complex [more info...] Chain information for diana-min.pdb #1 --- Chain | Description | UniProt A | epidermal growth factor receptor | EGFR_HUMAN close session open ""C:\Users\ricar\Downloads\Ejemplo DGE\Diabetes\Docking-EGFR\diana- min.pdb"" format pdb Summary of feedback from opening C:\Users\ricar\Downloads\Ejemplo DGE\Diabetes\Docking-EGFR\diana-min.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK File generated by Swiss-PdbViewer 4.00b0 Ignored bad PDB record found on line 2 REMARK http://www.expasy.org/spdbv/ Ignored bad PDB record found on line 4951 SPDBVT 1.0000000000 0.0000000000 0.0000000000 Ignored bad PDB record found on line 4952 SPDBVT 0.0000000000 1.0000000000 0.0000000000 Ignored bad PDB record found on line 4953 SPDBVT 0.0000000000 0.0000000000 1.0000000000 240 messages similar to the above omitted diana-min.pdb title: The egf-bound EGFR/HER2 ectodomain complex [more info...] Chain information for diana-min.pdb #1 --- Chain | Description | UniProt A | epidermal growth factor receptor | EGFR_HUMAN close session open ""C:/Users/ricar/Downloads/Ejemplo DGE/Diabetes/Docking-EGFR/Erlotinib- min.pdb"" addH Unknown command: addH addh Summary of feedback from adding hydrogens to Erlotinib-min.pdb #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 0 hydrogens added addcharges Unknown command: addcharges addcharge Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\ricar\AppData\Local\Temp\tmp5v_qgpfr\ante.in.mol2 -fi mol2 -o C:\Users\ricar\AppData\Local\Temp\tmp5v_qgpfr\ante.out.mol2 -fo mol2 -c bcc -nc 0 -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\ricar\AppData\Local\Temp\tmp5v_qgpfr\ante.in.mol2); atoms read (52), bonds read (54).` (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: 208; net charge: 0` (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!` Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 319, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\cmd.py"", line 31, in cmd_addcharge add_charges(session, residues, method=method, status=session.logger.status, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 26, in add_charges add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms), File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 334, 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 598, 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 598, in nonstd_charge raise ChargeError(ante_failure_msg) See log for complete Python traceback. addcharge Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\ricar\AppData\Local\Temp\tmp994h_jkr\ante.in.mol2 -fi mol2 -o C:\Users\ricar\AppData\Local\Temp\tmp994h_jkr\ante.out.mol2 -fo mol2 -c bcc -nc 0 -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\ricar\AppData\Local\Temp\tmp994h_jkr\ante.in.mol2); atoms read (52), bonds read (54).` (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: 208; net charge: 0` (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!` Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 319, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\cmd.py"", line 31, in cmd_addcharge add_charges(session, residues, method=method, status=session.logger.status, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 26, in add_charges add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms), File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 334, 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 598, 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 598, in nonstd_charge raise ChargeError(ante_failure_msg) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 30.0.101.2079 OpenGL renderer: Intel(R) UHD Graphics OpenGL vendor: Intel Python: 3.9.11 Locale: es_MX.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP All-in-One 24-df0xxx OS: Microsoft Windows 11 Home Single Language (Build 22621) Memory: 8,407,236,608 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i3-10110U CPU @ 2.10GHz OSLanguage: es-MX Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.0.5 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RIBFIND: 0.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0" defect closed moderate Structure Editing fixed all ChimeraX