[gmx-users] Simulating beta-peptides

[Justin Lemkul]

On 7/22/14, 9:59 AM, Venkat Reddy wrote:
> Dear Gromacs users,
> Can I use GROMOS53A6 ff for simulating beta-peptides? I found some articles
> on beta peptide simulations using GROMOS53A6 and 53A7 ff. Do I have to edit
> any  dihedral angle info to process my beta peptide after pdb2gmx step?
>

You'll have to write new force field files, the .rtp at minimum, because 
beta-peptide connectivity is different.  There may be new bonded parameters 
involved, but those should be described in the literature.

-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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