isolde sim start: OpenMM error

[apate31@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
> remotecontrol rest start port 53967

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
REST server started on host 127.0.0.1 port 53967  
Visit http://127.0.0.1:53967/cmdline.html for CLI interface  

> volume #2 level 0.05388

> volume #2 step 1

> ui tool show Toolbar

> surface dust #2 size 10.8

> ui tool show "Model Panel"

> hide #!2 models

> addh

Summary of feedback from adding hydrogens to
MBP_SHP55_trimer_modelAF_DNR2_refined_004-coot-0_real_space_refined_005coot_real_space_refined_006.pdb
#1  
---  
warnings | Not adding hydrogens to /A LYS 1 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to /A ILE 2 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 3 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A SER 270 CB because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | No usable SEQRES records for MBP_SHP55_trimer_modelAF_DNR2_refined_004-coot-0_real_space_refined_005coot_real_space_refined_006.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for
MBP_SHP55_trimer_modelAF_DNR2_refined_004-coot-0_real_space_refined_005coot_real_space_refined_006.pdb
(#1) chain B; guessing termini instead  
No usable SEQRES records for
MBP_SHP55_trimer_modelAF_DNR2_refined_004-coot-0_real_space_refined_005coot_real_space_refined_006.pdb
(#1) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A LYS 1, /B LYS 1, /C LYS 1  
Chain-initial residues that are not actual N termini: /A LEU 463, /B LEU 463,
/C LEU 463  
Chain-final residues that are actual C termini: /A ARG 576, /B ARG 576, /C ARG
576  
Chain-final residues that are not actual C termini: /A VAL 429, /B VAL 429, /C
VAL 429  
1014 hydrogen bonds  
3 hydrogens added  
  

> hide HC

> clipper associate #2 toModel #1

Opened DeepEMhancer_global_cryosparc_P29_J254_map_sharp.mrc as #1.1.1.1, grid
size 306,306,306, pixel 1.08, shown at level 0.261, step 1, values float32  
Chain information for
MBP_SHP55_trimer_modelAF_DNR2_refined_004-coot-0_real_space_refined_005coot_real_space_refined_006.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
1.2/C | No description available  
  

> select #1

25327 atoms, 25648 bonds, 3 pseudobonds, 1629 residues, 8 models selected  

> isolde sim start sel

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 52 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/anamika/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 122, in isolde_sim  
isolde.start_sim()  
File "/Users/anamika/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/isolde.py",
line 896, in start_sim  
sm.start_sim()  
File "/Users/anamika/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/Users/anamika/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/Users/anamika/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1364, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/openmm.py", line 19448, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: There is no registered Platform called "HIP"  
  
openmm.OpenMMException: There is no registered Platform called "HIP"  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/openmm.py", line 19448, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> 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  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac16,9
      Model Number: Z1CD0014GLL/A
      Chip: Unknown
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 3 days, 22 hours, 38 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: D6950CQMG2
          Display Firmware Version: Version 16.4 (Build 20E246)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        DELL S2421HGF:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 144.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
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    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.25.2
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
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    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
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    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
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    comm: 0.2.2
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    imagecodecs: 2024.6.1
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    ipykernel: 6.29.5
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    Jinja2: 3.1.6
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    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Reported by Anamika Patel