Hi, I have a .pdb file that I generated by creating three more copies of the protein according to its P212121 symmetry. I am now trying to run pdb2gmx on it, but I get the following error:
Fatal error: Residue 111 named CYS of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. What is weird is that there is no residue 111 that is a cysteine (residue 111 is a phenylalanine). I had run MD simulations successfully on a single copy of this protein before. pdb2gmx runs without an error when I use the old .pdb file. What could be the problem? Best, Irem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
