GROMACS version:2020.3-gpu-mpi
I was trying to convert a PEGylated polymer pdb into gro file, but I got an error saying that “residue ‘PEG’ not found in residue topology database”. I changed the residue name to “LIG” and “HET”, but neither of them worked. The forcefield I am using is OPLS4. For these kind of non-amino acid molecules, what residue name should I use?
Force fields can only produce topologies for species they recognize. PEG is not likely built in to any existing biomolecular force field, so you would need to parametrize it and build the corresponding residue topology.