[gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

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 <jalemkul at vt.edu> To:
> Discussion list for GROMACS users <gmx-users at 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

========================================