Hi, Like it says, you'll need to understand why pdb2gmx expects O5' but your coordinate file doesn't have one. We can't see your files or understand the context of residue 9.
Mark On Tue, Jul 11, 2017 at 2:14 PM maria khan <mariabiochemi...@gmail.com> wrote: > Dear gromacs user. > > i am simulating protein having DNA ,,when i applied for pdb to gmx > command,it gives me error like """Residue 9 named DG of a molecule in the > input file was mapped > to an entry in the topology database, but the atom O5' used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed.""" > > while using charmm27 all-atom ff.By using gromos 96 43a1 ff, it doesnt form > topology for DNA > > kindly give me a detail answer. > > thanks > -- > 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.
