isolde sim start: OpenMMException: Error compiling kernel

[513367167@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

> ui tool show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  

Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> open "E:/study/structure_bijiben_huashuo/Lc-motilin and GHSR coot and
> phenix/maximum466_467_sharp.mrc"

Opened maximum466_467_sharp.mrc as #1, grid size 360,360,360, pixel 0.73,
shown at level 0.00112, step 2, values float32  

> open "E:/study/structure_bijiben_huashuo/Lc-motilin and GHSR coot and
> phenix/jingxiu2 refine120 coot.pdb"

Chain information for jingxiu2 refine120 coot.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 81 residues in model #2 to IUPAC-IUB
standards.  
Chain information for jingxiu2 refine120 coot.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
2.2/F | No description available  
2.2/G | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  

> clipper associate #1 toModel #2

Opened maximum466_467_sharp.mrc as #2.1.1.1, grid size 360,360,360, pixel
0.73, shown at step 1, values float32  

> isolde sim start /C-D,F-G,E,B,A

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #2.2

Summary of feedback from adding hydrogens to jingxiu2 refine120 coot.pdb #2.2  
---  
notes | No usable SEQRES records for jingxiu2 refine120 coot.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for jingxiu2 refine120 coot.pdb (#2.2) chain B;
guessing termini instead  
No usable SEQRES records for jingxiu2 refine120 coot.pdb (#2.2) chain C;
guessing termini instead  
No usable SEQRES records for jingxiu2 refine120 coot.pdb (#2.2) chain D;
guessing termini instead  
No usable SEQRES records for jingxiu2 refine120 coot.pdb (#2.2) chain E;
guessing termini instead  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PHE 1, /B PRO 41, /C THR
4, /D LEU 7, /E SER 8, /F GLN 1, /G VAL 2  
Chain-initial residues that are not actual N termini: /B LYS 157, /B HIS 258,
/C THR 181, /G ASP 137  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A MET 14, /B LEU 337, /B
ALA 151, /B ARG 241, /C VAL 361, /C HIS 57, /D SER 342, /E ARG 62, /F VAL 126,
/G LEU 247, /G SER 120  
1069 hydrogen bonds  
Adding 'H' to /B LYS 157  
Adding 'H' to /B HIS 258  
Adding 'H' to /C THR 181  
Adding 'H' to /G ASP 137  
/A MET 14 is not terminus, removing H atom from 'C'  
/B LEU 337 is not terminus, removing H atom from 'C'  
/C VAL 361 is not terminus, removing H atom from 'C'  
/D SER 342 is not terminus, removing H atom from 'C'  
/E ARG 62 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
9916 hydrogens added  
  

> isolde sim start
> /A:2-13/B:42-150,158-240,259-336/C:5-56,182-360/D:8-341/E:9-61/F:2-125/G:3-119,138-246

Traceback (most recent call last):  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\toolbar\tool.py", line
205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\info.py",
line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1306, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 184, in run_provider  
toolbar_command(session, name)  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py",
line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\Administrator\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\openmm\app\simulation.py", line
103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\openmm\openmm.py", line 4584, in
__init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel:  
  
openmm.OpenMMException: Error compiling kernel:  
  
File "E:\ChimeraX 1.8\bin\Lib\site-packages\openmm\openmm.py", line 4584, in
__init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  




OpenGL version: 3.3.0 NVIDIA 425.46
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: TUF GAMING FX504GD_FX80GD
OS: Microsoft Windows 10 专业版 (Build 18362)
Memory: 34,207,600,640
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
OSLanguage: zh-CN

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
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    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
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    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
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    ChimeraX-Mole: 1.0
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    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
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    ChimeraX-SmoothLines: 1.0
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    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
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    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
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    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
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    imagesize: 1.4.1
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    superqt: 0.6.3
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    tifffile: 2024.1.30
    tinyarray: 1.2.4
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    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1