On 6/27/12 2:05 PM, Shima Arasteh wrote:
:)) 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?
The decision should not be whether or not there is an N-formylation on your
protein. It seems obvious that you need it. The real issue is how it is
represented, which entails two issues:
1. A parent force field to use
2. Parameterization of the formyl group under the rules of the parent force
field
The mechanics within Gromacs are irrelevant to these concerns and only matter
once those points are satisfied. No matter the force field you choose, the
assembly of the topology through pdb2gmx is the same.
-Justin
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
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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
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