id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
10449	QOpenGLShader::compile: syntax error	petersx1@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Hi there,

I am trying to run antechamber on my ligand and add a AM1-BCC charge. However I keep getting an error. I have searche the internet and also tried to follow the suggestions but they do not work. Please could you assist?

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue 0 (net charge -3) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2 -fi mol2 -o C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.out.mol2 -fo mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(0)
(0) Welcome to antechamber 20.0: molecular input file processor.
(0)
(0) Info: Finished reading file (C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2); atoms read (46), bonds read (48).
(0) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(0) bash.exe: warning: could not find /tmp, please create!
(0)
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(0) bash.exe: warning: could not find /tmp, please create!
(0) Info: Total number of electrons: 260; net charge: -3
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out
(0) bash.exe: warning: could not find /tmp, please create!
(0) /usr/bin/antechamber: Fatal Error!
(0) Cannot properly run """"C:/Program Files/ChimeraX/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: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -i C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2 -fi mol2 -o C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.out.mol2 -fo mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(0)
(0) Welcome to antechamber 20.0: molecular input file processor.
(0)
(0) Info: Finished reading file (C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2); atoms read (46), bonds read (48).
(0) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(0) bash.exe: warning: could not find /tmp, please create!
(0)
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(0) bash.exe: warning: could not find /tmp, please create!
(0) Info: Total number of electrons: 260; net charge: -3
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out
(0) bash.exe: warning: could not find /tmp, please create!
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc"" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p ""C:/Program Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT"" -s 2 -j 1
(0) bash.exe: warning: could not find /tmp, please create!
(0)
(0) Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(0) bash.exe: warning: could not find /tmp, please create!
(0)
Charges for residue 0 determined

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' : syntax error
syntax error  
  
  

*** Problematic Fragment shader source code ***  
#version 110  
#ifdef GL_KHR_blend_equation_advanced  
#extension GL_ARB_fragment_coord_conventions : enable  
#extension GL_KHR_blend_equation_advanced : enable  
#endif  
#define lowp  
#define mediump  
#define highp  
#line 1  
varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool
swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor =
texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor =
swizzle ? tmpFragColor.bgra : tmpFragColor;}  
***  

> open C:\Users\User\Documents\kerinew\system5\complex.pdb format pdb

Chain information for complex.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> select #1.2/A

10683 atoms, 10811 bonds, 672 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show ""Add Hydrogens""

[Repeated 1 time(s)]

> addh #1.1

Summary of feedback from adding hydrogens to complex.pdb #1.1  
---  
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  
11 hydrogens added  
  

> ui tool show ""Add Charges""

Closest equivalent command: addcharge & sel standardizeResidues
5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue 0 (net charge -3) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2 -fi mol2 -o
C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.out.mol2 -fo mol2 -c bcc -nc
-3 -j 5 -s 2 -dr n  
(0) ``  
(0) `Welcome to antechamber 20.0: molecular input file processor.`  
(0) ``  
(0) `Info: Finished reading file
(C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2); atoms read (46),
bonds read (48).`  
(0) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) ``  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) `Info: Total number of electrons: 260; net charge: -3`  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o
sqm.out`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) `/usr/bin/antechamber: Fatal Error!`  
(0) `Cannot properly run """"C:/Program Files/ChimeraX/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: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -i
C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2 -fi mol2 -o
C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.out.mol2 -fo mol2 -c bcc -nc
-3 -j 5 -s 2 -dr n  
(0) ``  
(0) `Welcome to antechamber 20.0: molecular input file processor.`  
(0) ``  
(0) `Info: Finished reading file
(C:\Users\User\AppData\Local\Temp\tmpq4cnj_qu\ante.in.mol2); atoms read (46),
bonds read (48).`  
(0) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) ``  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) `Info: Total number of electrons: 260; net charge: -3`  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o
sqm.out`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc"" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p ""C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT"" -s 2 -j 1`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) ``  
(0) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(0) `bash.exe: warning: could not find /tmp, please create!`  
(0) ``  
Charges for residue 0 determined  




OpenGL version: 3.3.0 - Build 20.19.15.4549
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_ZA.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 8700
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 17,093,038,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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
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    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
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    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    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
    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: 1.5.13
    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: 1.0.3
    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: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
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    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
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    pure-eval: 0.2.2
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    Pygments: 2.16.1
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    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
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    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
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    snowballstemmer: 2.2.0
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    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1
File attachment: complex.pdb

}}}

[attachment:""complex.pdb""]
"	defect	feedback	normal		Graphics				Tom Goddard				all	ChimeraX