[gmx-users] Ligand RMSD greater than Protein C alpha RMSD

Justin Lemkul jalemkul at vt.edu
Wed May 7 19:09:45 CEST 2014

On 5/7/14, 12:42 PM, MUSYOKA THOMMAS wrote:
> Dear Users,
> I am doing protein-ligand MD simulations and came across rather unusual
> result where the Ligand's RMSD is greater than that of the C alpha backbone
> of the protein in which it is docked into. Does this happen under usual
> circumstances?

That depends on how you measure the RMSD, particularly with respect to what your 
fitting group was.



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


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