[gmx-users] Query of RMSD results

Justin Lemkul jalemkul at vt.edu
Wed Oct 29 14:37:47 CET 2014

On 10/29/14 9:34 AM, Sainitin Donakonda wrote:
> Dear Micholas,
> Thanks for reply, I used g_rms routine
> As per my knowledge i understand that if protein  ligand complex has high
> RMSD over protein only RMSD then it means that ligand has some influence on
> protein backbone.
> But in my case i saw low RMSD value for protein-ligand in comparision to
> protein only . Now i am confused what to interpret for this result. Can you
> please suggest some insights?

The term "some influence" is far too generic.  Either a ligand has a stabilizing 
effect (protein RMSD in complex < apo RMSD) or a destabilizing effect (protein 
RMSD in complex > apo RMSD).  The small difference you calculated may or may not 
be significant, but you will have to do more analysis and/or more simulations to 
get a full picture of what's going on.



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


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