[gmx-users] lipid-protein simulation

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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