Dear Gromacs users, I have built a pdb file format for a polymer, and I want to use GROMOS FF. Therefore, I included polar Hydrogens in the pdb file, but I do not know how to name CH2 groups in NAME and SEGNAME columns. When executing the pdbtogmx command I receive the following error: Residue 2 named DEP of a molecule in the input file was mapped to an entry in the topology database, but the atom CH2 used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
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