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Topology.from pdb fails on deprotonated cysteine (CYM)

Topology.from pdb fails on deprotonated cysteine (CYM): a task in MiMo-V2.6-RL-oss: Agentic RL Environments (MiMo RL release). Topology.from pdb fails on deprotonated cysteine (CYM) I'm trying to load a protein PDB into an OpenFF Topology for parameterization. The structure has one cysteine where…

The task

Topology.from_pdb fails on deprotonated cysteine (CYM) 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…

Part of XiaomiMiMo/MiMo-V2.6-RL-oss.