[gmx-users] Query of RMSD results
saigro16 at gmail.com
Mon Nov 3 20:45:59 CET 2014
Thanks for clarification. Here i send weblink which contains RMSD plot of 5
protein-ligand complexes along with protein only after MD.
This plot shows that protein-ligand1 complex is little below in comparision
to Protein only. I am not able to understand why only this protein-ligand 1
complex is like this.
Can you please help me what to interpret this RMSD plot.
On Wed, Oct 29, 2014 at 2:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> 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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