[gmx-users] What might be the process if we wanted to sim a peptide + a peptide?

[Justin A. Lemkul]

swati shah wrote:
> Hi Justin,
> 
> Thanks for your support. I am new user of Gromacs. Can you provide some 
> information about binding of peptides with the small molecule causing a 
> PTM event?
> 

Again, the question you ask is far too broad to really elicit a useful response. 
  I know nothing about what you're trying to do, but this is not really the 
forum for anyone to tell you how to do your research.

Usually, when one thinks of the influence of small molecules on 
post-translational modifications (again, assuming that's what you mean by PTM), 
the process involves some sort of event where the small molecule binds a 
receptor or target enzyme, which may then become modified itself, and then exert 
its effect (catalyze a reaction on a substrate).  Perhaps you can look at some 
sorts of small molecule-enzyme binding and/or enzyme-substrate binding, but 
certainly MD is not capable of modeling any sort of pathway, and classical MD 
(as I said before) cannot handle any sort of reaction that might occur.

-Justin

> 
> --- On *Fri, 10/12/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] What might be the process if we wanted to
>     sim a peptide + a peptide?
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Friday, 10 December, 2010, 3:42 AM
> 
> 
> 
>     swati shah wrote:
>      > Dear Gromacs Users,
>      >
>      > Can we perform gromacs analysis on any two molecules like
>     peptide+ peptide or DNA+ RNA? and what might be the setup and
>     process if we wanted to sim a peptide + a peptide with a small
>     molecule causing a PTM event. If we can do so then do we have any
>     options to select two peptides with one or more having PTM via small
>     molecule. What might be the sequence of events in this use case.
>      > Any suggestion??
>      >
> 
>     Your series of questions is extremely broad, especially the use of
>     the phrase "Gromacs analysis."  What do you mean?  Do you wish to
>     study the effect of a post-translational modification (PTM) on
>     peptide aggregation?  Or binding studies of peptides and nucleic acid?
> 
>     In theory, you can set up just about anything you want.  Gromacs is
>     versatile like that.  If you're looking at covalent PTM events, then
>     no, you can't do it with classical mechanics, which does not allow
>     for bond breaking or forming.  If you want to study the effects of
>     small molecules on aggregation, that's also possible.  The
>     conditions depend entirely upon what's known about such a system.
> 
>     If you ask a more focused, specific question, you're more likely to
>     get a real answer.
> 
>     -Justin
> 
>      > Thanks,
>      > SWati
>      >
>      >
> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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