:)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree?
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: > 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? > Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
