[gmx-users] Re: pdb2gmx error

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jun 27 20:05:00 CEST 2012

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?


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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