Amber forcefields use terminal residues that are parametrized differently from normal ones. You can't just label a few atoms as the terminal ones and have it work; you need a whole residue, and this makes a single-residue zwitterion topology impossible to build with pdb2gmx. You need to cap the termini, or use two residues, or some other topology building tool.
Mark On Mar 24, 2014 8:26 AM, "virk" <virkbl...@yahoo.com> wrote: > Dear People, > > I am trying to simulate glycine molecule using amber ff. I have changed the > residues in pdb file with N and C respectively. > ATOM 1 N NGLY 1 -1.476 0.232 0.252 1.00 0.00 > ATOM 2 CA CGLY 1 -0.012 0.296 0.348 1.00 0.00 > ATOM 3 C CGLY 1 0.596 -0.652 -0.648 1.00 0.00 > ATOM 4 O GLY 1 -0.124 -1.320 -1.368 1.00 0.00 > ATOM 5 OXT GLY 1 1.916 -0.760 -0.740 1.00 0.00 > ATOM 6 H3 GLY 1 -1.736 -0.252 -0.592 1.00 0.00 > ATOM 7 HA2 GLY 1 0.292 0.020 1.364 1.00 0.00 > ATOM 8 HA1 GLY 1 0.320 1.320 0.132 1.00 0.00 > ATOM 9 H GLY 1 -1.636 -0.236 1.132 1.00 0.00 > ATOM 10 H GLY 1 -1.916 1.136 0.272 1.00 0.00 > TER 11 GLY 1 > END > > But when I am using pdb2gmx, I am getting this error > Residue 1 named NGLY 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. > > But atom CA is in the input pdb file and with same name in amber .rtp file > too. If I remove N and C prefixes in pdb file, pdb works for all other > fields. > > I will be thankful for your help and time. > > Kind Regards, > Amninder Virk > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/amber-ff-gromacs-tp5015342.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- 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.