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

[Justin Lemkul]

On 8/12/14, 10:52 AM, Wainwright, Josh wrote:
> Hello everybody,
>
> I am trying to find some archaeal lipid packages to work in Gromss 53A6 forcefield and have only come across those on the website lipid book:
>
> http://lipidbook.bioch.ox.ac.uk/package/show/id/20.html
>
> Unfortunately these lipid parameters are not working quite as we expected and give a very large RMSD for our protein in the system which we believe the lipid parameters are to blame.
>

Does the protein have a high helical content?  If so, then it's the 53A6 protein 
parameters that are to blame; that force field is known to understabilize 
helices, in some cases dramatically.

-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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