ISOLDE: start sim: OpenMMException: Error compiling kernel

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

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/jbp20/OneDrive - Imperial College London/3 RESEARCH PROJECTS
> IN
> PROGRESS/Pici/20240213_Pici_sessionwithAra/20240212_PICImodel_ramachandran4-coot-2.pdb"

Chain information for 20240212_PICImodel_ramachandran4-coot-2.pdb #1  
---  
Chain | Description  
1 2 3 4 | No description available  
  

> open "C:/Users/jbp20/OneDrive - Imperial College London/3 RESEARCH PROJECTS
> IN
> PROGRESS/Pici/20240213_Pici_sessionwithAra/Asymetric_combination_coot2.ccp4"

Opened Asymetric_combination_coot2.ccp4 as #2, grid size 183,183,183, pixel
1.43, shown at level 0.988, step 1, values float32  

> color #2 #b2b2b2d7 models

> color #2 #3a3a3ad7 models

> color #2 #00aa00d7 models

> color #2 #002600d7 models

> color #2 #00a700d7 models

> transparency 80

> isolde start

> 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Forcefield cache not found or out of date.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 Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 20240212_PICImodel_ramachandran4-coot-2.pdb  
---  
Chain | Description  
1.2/1 1.2/2 1.2/3 1.2/4 | 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  

> fitmap #1 inMap #2

Fit molecule 20240212_PICImodel_ramachandran4-coot-2.pdb (#1.2) to map
Asymetric_combination_coot2.ccp4 (#2) using 18252 atoms  
average map value = 0.6349, steps = 44  
shifted from previous position = 0.0347  
rotated from previous position = 0.0553 degrees  
atoms outside contour = 14372, contour level = 0.9881  
  
Position of 20240212_PICImodel_ramachandran4-coot-2.pdb (#1.2) relative to
Asymetric_combination_coot2.ccp4 (#2) coordinates:  
Matrix rotation and translation  
0.99999954 0.00062079 -0.00073625 -0.06655213  
-0.00062075 0.99999981 0.00005240 0.31984025  
0.00073628 -0.00005194 0.99999973 -0.32326270  
Axis -0.05409119 -0.76340401 -0.64365244  
Axis point 467.42441268 0.00000000 -93.07573160  
Rotation angle (degrees) 0.05525882  
Shift along axis -0.03249863  
  

> clipper associate #1 toModel #2

Invalid "toModel" argument: must specify 1 structure, got 0 for "#2"  

> clipper associate #2 toModel #1

Opened Asymetric_combination_coot2.ccp4 as #1.1.1.1, grid size 183,183,183,
pixel 1.43, shown at step 1, values float32  

> select clear

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde sim start /1-4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\\__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\openmm\app\simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCLC318.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCLC318.tmp.cl".  
Frontend phase failed compilation.  
  
  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCLC318.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCLC318.tmp.cl".  
Frontend phase failed compilation.  
  
  
File "C:\Program Files\ChimeraX\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.  
  

> isolde sim start /1-4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\\__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\openmm\app\simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCL39D.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCL39D.tmp.cl".  
Frontend phase failed compilation.  
  
  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCL39D.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCL39D.tmp.cl".  
Frontend phase failed compilation.  
  
  
File "C:\Program Files\ChimeraX\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.  
  

> ui tool show "Ramachandran Plot"

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> isolde pepflip /4:191

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\\__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\toolbar.py", line 37, in toolbar_command  
run(session, f'isolde pepflip {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\manipulations\cmd.py", line 37, in pep_flip  
isolde_sim(session, 'start', residues.atoms)  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\jbp20\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\openmm\app\simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py", line
4584, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCLB700.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCLB700.tmp.cl".  
Frontend phase failed compilation.  
  
  
openmm.OpenMMException: Error compiling kernel:
"C:\Users\jbp20\AppData\Local\Temp\OCLB700.tmp.cl", line 31: error: attributes  
may not appear here  
__attribute__((overloadable)) unsigned long atom_add(volatile __global
unsigned long* p, unsigned long val) {  
^  
  
1 error detected in the compilation of
"C:\Users\jbp20\AppData\Local\Temp\OCLB700.tmp.cl".  
Frontend phase failed compilation.  
  
  
File "C:\Program Files\ChimeraX\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.  
  




OpenGL version: 3.3.13411 Core Profile Forward-Compatible Context 15.201.2401.1001
OpenGL renderer: AMD RADEON HD 6450
OpenGL vendor: ATI Technologies Inc.

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

Manufacturer: Hewlett-Packard
Model: HP Compaq 8200 Elite SFF PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 8,545,853,440
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
OSLanguage: en-GB

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-Clipper: 0.22.4
    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-ISOLDE: 1.7.1
    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

[Tristan Croll]

Looks like an idiosyncrasy of the AMD OpenCL driver. If I recall correctly this has come up before and I've raised it with Peter Eastman, and it should be fixed in the next OpenMM version.