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Charge assignment with ambertools failing on ubuntu with python 3.10 in examples CI #2020

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j-wags opened this issue Feb 11, 2025 · 0 comments

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j-wags commented Feb 11, 2025

https://github.com/openforcefield/openff-toolkit/actions/runs/13253018566/job/36994725943

=================================== FAILURES ===================================
___________ examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 9 ___________
[gw1] linux -- Python 3.10.16 /home/runner/micromamba/envs/rdkit-examples/bin/python
Notebook cell execution failed
Cell 9: Cell execution caused an exception

Input:
interchange = sage_ff14sb.create_interchange(top)

...

File ~/micromamba/envs/rdkit-examples/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py:280, in ToolkitRegistry.call(self, method_name, raise_exception_types, *args, **kwargs)
    278 for toolkit, error in errors:
    279     msg += f" {toolkit} {type(error)} : {error}\n"
--> 280 raise ValueError(msg)

ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '163' and SMILES '[H][O][C@@]1([H])[c]2[c]([c]([O][c]3[c]([H])[c]([F])[c]([H])[c]([C]#[N])[c]3[H])[c]([H])[c]([H])[c]2[S](=[O])(=[O])[C]([H])([H])[H])[C]([H])([H])[C]1([F])[F]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2024.03.5, ToolkitWrapper around AmberTools version 23.6, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around The RDKit version 2024.03.5 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are {'mmff94': {}, 'gasteiger': {}}
 ToolkitWrapper around AmberTools version 23.6 <class 'subprocess.CalledProcessError'> : Command '['antechamber', '-i', 'molecule.sdf', '-fi', 'sdf', '-o', 'charged.mol2', '-fo', 'mol2', '-pf', 'yes', '-dr', 'n', '-c', 'bcc', '-nc', '0.0']' returned non-zero exit status 1.
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" is not supported by the Built-in toolkit. Available charge methods are {'zeros': {'rec_confs': 0, 'min_confs': 0, 'max_confs': 0}, 'formal_charge': {'rec_confs': 0, 'min_confs': 0, 'max_confs': 0}}
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