[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

You are right. 

OK, the reason of adding FOR is what I explained a few minutes ago.
All over, I'm supposed to use a modern FF . ( In similar researches I found CHARMM is suitable, so I would add FOR as the procedure explained in GROMACS.ORG) 

For now, because I wanna regenerate an old simulation, I keep the FOR, then here it's stopped! Seeking for a solution!

If any suggestion, I look forward hearing from you.
THANKS FOR ALL YOUR KIND REPLIES! :)

 
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 10:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



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

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


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