[gmx-users] membrane protein simulation

[Samik Bhattacharya]

Thanx Justin...i must go throuh that tutorial. thanx for the help. 

--- On Fri, 29/5/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] membrane protein simulation
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, 29 May, 2009, 4:49 PM



Samik Bhattacharya wrote:
> hi  i'm new to gromacs and want to simulate a protein inside a phospholipid envelop (may be box or dodecahedron). for this i got the pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems in generating the topology files as well as in running grompp as gromacs does not support lipids. i also tested it by using the lipid.itp file in the top directory. can anyone suggest me any tutorial where i can find detailed discussion on this matter? and obviously some help in how to go for it??

Yes, there is a tutorial here:

http://wiki.gromacs.org/index.php/Membrane_Simulations#Running_Membrane_Simulations

-Justin

> Thanking you in advance
> Shamik
> 
> 
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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