Dear Shounak, So what's about the FOR residue? I can't eliminate it. I guess if I do as you suggest, I need to add the FOR to n.tdb and then the procedure would be different! Yes, I added the FOR to rtp file on my own.
Sincerely, Shima ----- Original Message ----- From: shounakb <bane...@rpi.edu> To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:22 PM Subject: [gmx-users] Re: pdb2gmx error Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Sincerely, Shounak -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
