Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning:
WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CB used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here? 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.
