[gmx-users] Protein Membrane SImulation using CHARMM 36 forcefield

[Justin Lemkul]

On 10/3/16 10:43 AM, Roshan Shrestha wrote:
> I want to perform membrane protein simulation similar to justin's KALP
> tutorial, but using charmm 36 forcefield instead. I will be using POPC
> model membrane, the charmm36 based coordinates for which can be found in
> http://terpconnect.umd.edu/~jbklauda/research/download.html But, I am not
> sure if only coordinate files are sufficient to build the membrane since I
> could not find the other lipid parameters like POPC.itp and lipid.itp as
> such. How can I obtain these parameters as well for building my POPC
> membrane compatible to CHARMM 36 forcefield. Thanks
>

Use CHARMM-GUI.  It literally does everything for you, including writing 
topologies and GROMACS input files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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