[gmx-users] planarity restrain for ligand

[Justin Lemkul]

On 1/12/16 8:10 AM, ansuman at physics.iisc.ernet.in wrote:
> Dear Gromacs users,
>
> I am running an energy minimization on a protein ligand complex. The
> ligand is a nucleotide and after the em the base loses its planarity. I
> will be grateful if you let me know if a non-planar base is physically
> possible or not. If not, what procedure i have to follow to retain the
> planarity.
>

Bases are not completely planar; out-of-plane vibrations are reasonable.  Severe 
distortion, of course, is not.

-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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