[gmx-users] RMSF analysis

[Sainitin Donakonda]

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
>> showed
>> 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
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
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