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I have created my gro file in VMD , and now i’m looking for building topology file with the command gmx pdb2gmx -f graphene.gro -o processed.gro -p topol.top however i got this error Residue ‘GRA’ not found in residue topology database for all force field i choose how to do ?
I’m afraid I can’t give you any details how to do it, but pdb2gmx is not a suitable tool. See Fatal Error: Residue Not Found in the Residue Topology Database for a starting point, but unfortunately not a complete protocol.