openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
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Write ARG sidechain guanidinium SMARTS using wildcard bonds to match all resonance forms #29

Closed j-wags closed 4 years ago

j-wags commented 4 years ago

Closes #27

The produced FF now parameterizes both LYN_ARG and ALA_ARG, which should mean it captures both kekule forms of the ARG sidechain.

MainChain/LYN_ARG/LYN_ARG
HarmonicBondForce 9.76828670501709 kJ/mol
HarmonicAngleForce 8.674139022827148 kJ/mol
PeriodicTorsionForce 75.72264099121094 kJ/mol
NonbondedForce -720.9594116210938 kJ/mol
-626.7942504882812 kJ/mol
[H][C@@](C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=[N+]([H])[H])N([H])[H])(C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 8.674101829528809 kJ/mol
HarmonicBondForce 9.768287658691406 kJ/mol
NonbondedForce -720.9562377929688 kJ/mol
PeriodicTorsionForce 75.72282409667969 kJ/mol
-626.7911376953125 kJ/mol
201 amber dihedrals (10 impropers) and 201 off dihedrals

MainChain/ALA_ARG/ALA_ARG
HarmonicBondForce 9.490116119384766 kJ/mol
HarmonicAngleForce 7.35487699508667 kJ/mol
PeriodicTorsionForce 69.92710876464844 kJ/mol
NonbondedForce -665.9656372070312 kJ/mol
-579.1935424804688 kJ/mol
[H][C@@](C(=O)N([H])[C@]([H])(C(=O)N([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[N+](=C(N([H])[H])N([H])[H])[H])(C([H])([H])[H])N([H])C(=O)C([H])([H])[H]
HarmonicAngleForce 7.354863166809082 kJ/mol
HarmonicBondForce 9.490116119384766 kJ/mol
NonbondedForce -665.9627685546875 kJ/mol
PeriodicTorsionForce 69.92713928222656 kJ/mol
-579.190673828125 kJ/mol
164 amber dihedrals (10 impropers) and 164 off dihedrals