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openmm / openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)
http://openmm.org
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System Generator for Espaloma #352

Open chabi-fin opened 1 week ago

chabi-fin commented 1 week ago

I have espaloma installed, but I haven't been able to use it as an option for small_molecule_forcefield in a SystemGenerator. for, system_generator = SystemGenerator( forcefields=[ "amber/ff14SB.xml", "amber/tip3p_standard.xml", ], small_molecule_forcefield='espaloma-0.3.2', forcefield_kwargs=forcefield_kwargs, cache="db.json", ) I get the error: Source 'espaloma-0.3.2' could not be read. If this is a file, ensure that the path is correct. Looked in the following paths and found no files named 'espaloma-0.3.2': /home/lf1071fu/project_ip6/data/inputs/sire_test /home/lf1071fu/miniforge3/envs/espaloma/lib/python3.11/site-packages/openff/amber_ff_ports/offxml /home/lf1071fu/miniforge3/envs/espaloma/lib/python3.11/site-packages/openforcefields/offxml /home/lf1071fu/miniforge3/envs/espaloma/lib/python3.11/site-packages/smirnoff99frosst/offxml If 'espaloma-0.3.2' is present as a file, ensure it is in a known SMIRNOFF encoding. Valid formats are: ['XML'] Parsing failed while trying to parse source as a file with the following exception and message: <class 'openff.toolkit.utils.exceptions.SMIRNOFFParseError'> syntax error: line 1, column 0 If I use the option small_molecule_forcefield='openff-1.2.0' there is no error.

mattwthompson commented 1 week ago

Maybe use this https://github.com/openmm/openmmforcefields?tab=readme-ov-file#using-espaloma-to-generate-small-molecule-force-fields

mattwthompson commented 1 week ago

Otherwise something is wrong with your installation