[gmx-users] RMSF analysis
saigro16 at gmail.com
Wed Oct 9 22:09:43 CEST 2013
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
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.*
Let me know
On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/9/13 3:29 PM, Sainitin Donakonda wrote:
>> Hi all,
>> I recently performed MD simulation of protein - ligand complex..and
>> analyzed its trajectory using RMSF tool in gromacs.
>> This analysis revealed particular residue in binding site of protein
>> quite high fluctuation around 0.30 nm but other residues were in range of
>> 0.15 to 0.20
>> Can any body explain why this particular residue have high RMSF value in
>> compared to other residues
> Doubtful, at least not without considerably more information. What
> functional significance does it have, if any? What is the residue? What
> did you measure - RMSF of the whole residue, just the backbone, just
> C-alpha, etc?
> Higher RMSF means the residue flops around more, i.e. your outcome
> indicates that the residue deviates from the average position to a greater
> extent than the other residues. Whether or not this actually means
> anything at all depends on your knowledge of the nature of the
> protein-ligand complex and the answers to the questions posed above.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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