Hi Santhosh, Try renaming the atom (mind the space):
sed 's/OXT/O2 /' pdbfile > fixed.pdb And then run pdb2gmx on that. Cheers, Tsjerk On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan < santhoshraja...@gmail.com> wrote: > > This is the command I used > pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh > > And I used OPLS-AA/L all-atom force field.. > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TRP-with-24-at-tp5011015p5011219.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
