On 6/27/12 2:23 PM, Shima Arasteh wrote:
So as you said it doesn't matter to remove the FOR residue. But I can't
understand why the representation of FOR is still required!
I did not say that. Your last message gave the reason why the formyl group is
necessary. Have I misunderstood? This is all getting really confusing. If
you're adding a formyl cap, then you'd better have a reason for it, otherwise
all of this is a grand waste of time.
And, you suggest me to use another forcefield to produce the topology and
then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or
eliminate it? Honestly I'm a little confused here.
Yes, you should use a more reliable force field. You should choose it based on
significant reading about the pros and cons of different force fields and what
people generally use to simulate similar systems. You will then need to
re-derive parameters for the formyl group based on the parameterization
methodology required by the force field.
-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 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error
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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