ChargeError produces traceback

[chimerax-bug-report@…]

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