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openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
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Remove aromaticity(and probably formal charges and bond orders) from TRP sidechain #39

Closed j-wags closed 2 years ago

j-wags commented 2 years ago

Possibly related to #12

Under the MDL aromaticity model, the TRP and HIS sidechain rings aren't fully aromatic. To avoid confusion, we should ensure that the FF parameters that are intended to match these sidechains do not match based on aromaticity. In the 0.0.2 release, this isn't an issue for HIS (because that is solved using the resonance trick), but it is for TRP:

<Bond smirks="[H]c1c(c(c2[c:2](c1[H])[C:1](=C(N2[H])[H])C([H])([H])[C@@]([H])([C]=O)[N][H])[H])[H]" id="A14SB-MainChain_TRP-C*_CB" length="1.459 * angstrom" k="776.0 * angstrom**-2 * mole**-1 * kilocalorie"></Bond>
mattwthompson commented 2 years ago

All parameters now lack stereochemistry.