[gmx-users] lipid-protein simulation

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Sep 16 18:48:54 CEST 2012


Yes, I want to use the coordinate file from 50-ns simulation.  Would you please let me know what the criterion for knowing that the equilibrated system is proper for insertion of protein? Do the temperature, RMSD, pressure and visualization of popc-water system make me decide that it is a proper system or not?

Thanks for your suggestions dear Justin.



From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, September 16, 2012 9:08 PM
Subject: Re: [gmx-users] lipid-protein simulation

On 9/16/12 12:34 PM, Shima Arasteh wrote:
> Dear all,
> To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory.  I'm wondering:
>   1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water?

I will assume you mean the coordinate file is from a 50-ns simulation? Topologies are not time-dependent.  If you can demonstrate that your membrane is properly equilibrated in this time frame, then yes, it is a plausible starting model.

> 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions.

If you already have popc.itp then you don't need to run pdb2gmx.  What is lipid.itp?  If you're somehow thinking you need the Berger lipid parameters from Peter Tieleman, you don't.  CHARMM36 was built to handle lipids, so all necessary atom types, nonbonded, and bonded parameters should already be present in the force field, thus requiring no external modification.


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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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