Probably the default behaviour of pdb2gmx for termini is not appropriate for your input. Use pdb2gmx -ter and choose wisely
Mark On Nov 13, 2013 12:03 PM, "hasthi" <durgs7kr...@gmail.com> wrote: > Hello GROMACS users, > I have phosphorylated Serine residue in my > protein (140 residues) of interest, now when I run pdb2gmx I get this > following error > > Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms > while sorting atoms. > > I checked aminoacid.rtp, there is no separate entry for OXT there.When I > did the simulation for the same protein prior phosphorylation I did not get > this error. What is the reason for this and how should I rectify this > error? > > Please help me with this regard.... > > > Regards, > Hasthi > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
