[gmx-users] Query regarding membrane-peptide simulation

[Justin Lemkul]

On 8/19/13 6:27 AM, Aditya Padhi wrote:
> Dear Gromacs Users,
>          I am new to Gromacs. Recently, I started working with Gromacs. I
> want to study the mechanism of interaction of certain peptides that are
> known to interact with membranes such as DOPC, POPC and so on. I have two
> sets of peptides; out of which, one set of peptides are known to penetrate
> the membrane while the behavior of another set of peptides with the
> membrane is not known.
>          It would be really helpful if you can suggest me an appropriate
> tutorial on these lines. The most common query I have is to how to place
> and allow a peptide to cross or interact with the membrane? Shall I use VMD
> or any other software for this?
>          Please let me know your response.
>

There are many ways of placing molecules at specific locations within the unit 
cell.  editconf can do this.  There is no tutorial specifically for what you are 
trying to do, but you can generally get some guidance from:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

Note that you do not necessarily have to use a Gromos96 force field for your 
simulations; other force fields may perform better.  Do your homework first!

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html

The example editconf commands here should be instructive.

-Justin

> Thanking you,
> Regards
> Aditya.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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