[gmx-users] Archaeal lipid packages for Gromos 53A6

[Justin Lemkul]

On 8/12/14, 11:08 AM, Wainwright, Josh wrote:
> Thanks for the prompt response Justin. We are working with protein fragments with between 1 and 3 helices.
>
> I've noticed that Anirban Ghosh made a tutorial based on yours, and he used Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC in his case, as opposed to DPPC in your case with the model KALP-15 protein). Do you think 43a1 is a good alternative, or is there any other forcefield you would recommend?
>

43A1 or 54A7 would probably be better.

> I've also seen people recommend CHARMM36.
>

CHARMM36 has excellent lipid parameters, better than Berger for most observables.

-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 601
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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