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cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
GNU General Public License v3.0
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Fix atom typing errors when using OPLS #17

Open chrisjonesBSU opened 3 years ago

chrisjonesBSU commented 3 years ago

PEEK: gaff: Works opls: Error

Exception: Parameters have not been assigned to all proper dihedrals. Total system dihedrals: 174, Parameterized dihedrals: 158. Note that if your system contains torsions of Ryckaert-Bellemans functional form, all of these torsions are processed as propers.

PEKK: gaff: Works

opls: Error

Exception: Parameters have not been assigned to all proper dihedrals. Total system dihedrals: 180, Parameterized dihedrals: 154. Note that if your system contains torsions of Ryckaert-Bellemans functional form, all of these torsions are processed as propers.

So far, it looks like the errors are not being able to assign all of the dihedrals when using the opls forcefield.

If we pass assert_dihedral_params=False when using OPLS, then both PEEK and PEKK will work.

This fix won't require much within this repo, but rather with foyer. We could make a PR that adds missing dihedrals, but I'm not sure how long that would take.