pdb2gmx -ter On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj <vijayara...@gmail.com> wrote: > Hello, > > I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the > terminal residues from NALA and CALA to normal ALA (just as middle > residues). As the terminal selection option is not enabled with the amber > ff, I am using the termini modification parameters with aminoacids.c.tdb. > here is my code for the aminoacids.c.tdb > > [ COO- ] > > [ replace ] > H H 1.00800 0.27190 > N N 14.01000 -0.41570 > CA CT 12.01000 0.03370 > HA H1 1.00800 0.08230 > C C 12.01000 0.59730 > CB CT 12.01 -0.1825 > HB1 HC 1.008 0.0603 > HB2 HC 1.008 0.0603 > HB3 HC 1.008 0.0603 > > [ add ] > 1 1 O C CA N > O 16.00000 -0.56790 > > [ bonds ] > C O 1 0.12290 476976.0 > > [ delete ] > OC1 > OC2 > > > when I run pdb2gmx using this termini modification, everything works fine > except the deletion of OC1 and OC2 atoms, the error which I get for this run > as follows, > > Fatal error: > Atom OC2 not found in residue seq.nr. 8 while adding atom > > > any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ > delete ] option with the aminoacids.c.tdb file, it works fine by adding the > O atom to the terminal residue including the presence of OC1 and OC2 atoms. > first I am trying to modify the c terminal residue. > > Regards, > vijay. > > -- > 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 >
-- Best Regards, lina -- 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