[gmx-users] Berger lipid

[Justin A. Lemkul]

On 6/28/12 8:54 PM, Shima Arasteh wrote:
> Yes, I know that as studied the Kalp15 tutorial.
> Sorry, the last question :)
> :
>
>    DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok?  Because I see that POPC.itp is also required for simulation of protein in bilayer.
>

You need a topology of some sort.  It depends on what parameters you have on 
hand.  If you do not have popc.itp from anywhere, then you need to generate it 
somehow.  If it is present in the .rtp file for CHARMM36 that you have, then you 
can run pdb2gmx on it.

-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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