Topology.from pdb fails on deprotonated cysteine (CYM)

Topology.from pdb fails on deprotonated cysteine (CYM): a task in MiMo-V2.6-RL-harbor-code: MiMo-V2.6-RL Code (Harbor) (Harbor dataset). I'm trying to load a protein PDB into an OpenFF Topology for parameterization. The structure has one cysteine where the side-chain thiol is deprotonated (i.e…

The task

I'm trying to load a protein PDB into an OpenFF `Topology` for parameterization. The structure has one cysteine where the side-chain thiol is deprotonated (i.e. the SG carries a negative charge and there's no HG). In our PDB files this residue is labelled `CYM`, which is the convention used by AMBER / tleap and a few…

Part of FineEnvs/MiMo-V2.6-RL-harbor-code.