Comments (4)
I'm guessing this is the atom that Foyer is finding multiple types for. Determining which atom types get precedence (and thus which overrides you need) when an atom is part of multiple functional groups gets a bit tricky. In this case, however, my opinion would be that 'opls_713' should override 'opls_139'. This is something you would need to change in oplsaa.xml
(and could submit a PR while you're at it!). The OPLS force field in Foyer is obviously fairly incomplete, so we're hoping that as users begin to use various atom types it will begin to fill out.
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I wasn't sure if there was a way to do this without editing the oplsaa.xml
file by hand/if there was a way to do this programmatically, something like oplsaa.override(['opls_713'],['opls_139'])
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I don't think you can manually add overrides to a Forcefield object as this is intended to all be handled within the XML file.
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Yeah as @summeraz said, the intention is to have this contained in the xml file. We could think about implementing an interactive prompt for resolving overrides when you're creating a new forcefield but at the end of the day all the logic is intended to be captured in the file itself.
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Related Issues (20)
- `foyer.forcefield.apply` does not carry over atomic_number information from the input structure
- `Forcefield.get_parameters` returns empty lists for periodic torsions in the GAFF Forcefield HOT 1
- foyer.general_forcefield.Forcefield apply method results in improper parameter definition for lj epsilon HOT 1
- Broken links in README HOT 1
- Support for OpenMM HOT 3
- `ff.apply(verbose=True)` not printing out missing bonds
- Add more precision to the standard XMLs
- Incorrect handling of partially typed systems in general_forcefield.py HOT 1
- Edge case when scaling factors are 0 HOT 1
- Getting an error when using Porebuilder and foyer/mbuild, maybe in the box vectors. HOT 1
- Windows built is failing HOT 1
- Parametrized structure has non-zero charge. HOT 1
- ParmEd residue matching assumes ordered residues
- Atom typing triangular water fails HOT 3
- Improper dihedral coefficients in oplsaa.xml HOT 7
- The General Forcefield will not work with GMSO dev branch. HOT 1
- Foyer not working when installed using `conda` but works with `mamba` HOT 4
- Dihedrals not found HOT 13
- deep copy in nbfix doesn't preserve all structure attributes
- CI stops running because tests are using too much memory. #1090
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