I encountered a problem when I using pdb2gmx to convert a pdb file into gro and top file.by using 6: AMBER99SB-ILDN protein, nucleic AMBER94 Force field
The system give me a fatal error message as following:Atom P in residue DT 501 was not found in rtp entry DT5 with 30 atoms while sorting atoms. Before above mention fatal error system give fatal error Residue 37 named VAL of a molecule in the input file was mapped to an entry in the topology database, but the atom CG1 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed .While valine naming is same in .rtp entry and pdb file this error is remove but DT 501 fatal error still remaining -- 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.
