[gmx-users] RMSF analysis

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 22:21:27 CEST 2013

On 10/9/13 4:09 PM, Sainitin Donakonda wrote:
> What functional significance does it have, if any?  --- According to my
> knowledge this reside is present in binding site.. and forms some hydrogen
> bonds with ligand

Do you observe hydrogen bonds with the ligand?

> What is the residue?  -- *Glutamic Acid*
> What did you measure - RMSF of the whole residue, just the backbone, just
> C-alpha, etc? --* I measured Just C-alpha atoms.*

So the backbone is fairly flexible.  Glutamic acid residues are very flexible, 
though the flexibility is usually due to side chain motions, hence why they are 
among the more difficult residues to assign in crystal structures.  Depending on 
the extent to which this residue is solvent exposed, this may explain your 
observations.  But again, this is a complete guess and other factors may be 
significant here, including sampling time, whether or not you are eliminating 
some time at the start of the simulation to allow for unrestrained equilibration 
(VERY significant for quantities like RMSF), and whether or not the observation 
is reproducible in multiple simulations.  The RMSF value you report is not 
especially large and may not mean anything at all, and its absolute value may 
not be convincing of any sort of argument.  Whether or not it changes depending 
on conditions like presence or absence of a ligand may be more interesting, but 
as hopefully these last few sentences show, there is very little point in anyone 
guessing at functional implications from one vaguely described outcome ;)



Justin A. Lemkul, Ph.D.
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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