2024-07-19 Thompson/Wagner Check-in meeting notes

Owned by Jeffrey Wagner, created
Last updated: Jul 19, 2024
2 min read

Participants

  • @Matt Thompson

  • @Jeffrey Wagner

Discussion topics

Item

Notes

Item

Notes

General updates

  • MT –

    • PTO next Friday?

      • JW – Go for it

    • Torsion question - If I’m exporting from interchange, can I assume the torsions given by the toolkit are the torsions that should be written out? (that is, ProperTorsionHandler.find_matches is the final output), specifically

      • If ijkl is returned as a torsion, do I need to make sure these are actually bonded?

      • (We tried it out, turns out it raises an error)

from openff.toolkit import Molecule, ForceField from openff.units import unit ff = ForceField("openff-2.2.0.offxml") mol = Molecule.from_smiles("NCC=O") ff["ProperTorsions"].add_parameter({'smirks':'[H:1][N:2]C[C:3]=[O:4]', "k1":1.*unit.kilocalorie_per_mole, "periodicity1":1, "phase1":0*unit.degree} ) interchange = ff.create_interchange(mol.to_topology())

raises

File ~/conda/envs/off-tk-dev/lib/python3.10/site-packages/openff/interchange/smirnoff/_base.py:181, in _check_all_valence_terms_assigned(handler, assigned_terms, topology, valence_terms) 176 raise RuntimeError( 177 f"Could not find an exception class for handler {handler}", 178 ) 180 exception = exception_class(err_msg) --> 181 exception.unassigned_topology_atom_tuples = unassigned_atom_tuples 182 exception.handler_class = handler.__class__ 183 raise exception UnboundLocalError: local variable 'unassigned_atom_tuples' referenced before assignment

Trello

https://trello.com/b/dzvFZnv4/infrastructure

Action items

Decisions

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