I am using OPC water model in Amber parameters for my ChemShell QM/MM calculations. The OPC model has a dummy atom with an atom type of EP. I have verified the parse_amber.tcl file is reading the atom type EP and returns an atomic number of -1. However, the ChemShell output file warns “unknown atom types from amber prmtop: EP” and is leading to unstable MM energies in QM/MM optimisation job.
I have confirmed the OPC water as the source of unstable energies as - MM energies become stable if I exclude the water from the active region. Can you please suggest how to properly deal with dummy atom in OPC water model for QM/MM optimisation in ChemShell?