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

[swati shah]

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?

--- 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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