[gmx-users] Query of RMSD results

[Sainitin Donakonda]

Hi Justin,

Thanks for reply,  i plotted RMSF for all complexes and protein only please
check both RMSD and RMSF plot in following link.

http://sainitindonakonda.weebly.com/

Now in RMSF plot ligand 1 fluctuates slightly higher than protein-only. Im
confused :( i am not getting what to interpret for protein-ligand 1 complex
as it looks different in both RMSD and RMSF. Can you please give an
explanation on this point.  And also give more information about what is
the difference between RMSD and RMSF.

Thanks,
Sainitin




On Tue, Nov 4, 2014 at 1:25 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/3/14 2:45 PM, Sainitin Donakonda wrote:
>
>> Hi Justin,
>>
>> Thanks for clarification. Here i send weblink which contains RMSD plot of
>> 5
>> protein-ligand complexes along with protein only after MD.
>>
>> http://sainitindonakonda.weebly.com/
>> <http://www.google.com/url?q=http%3A%2F%2Fsainitindonakonda.weebly.
>> com%2F&sa=D&sntz=1&usg=AFQjCNFxheAJnTrgnrplxuOSiYe6ZVPJLw>
>>
>> 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.
>>
>>
> There's little to say from the plot aside from the fact that, in one
> trajectory, the protein in one particular complex deviates slightly less
> from the initial structure than does the apo structure.  There is no reason
> to presuppose that any ligand should inherently cause an increase in RMSD,
> viz. larger change in structure.  If you want to determine the reason
> behind it, you'll have to do more analysis on relevant structural features,
> like RMSF, hydrogen bonding, etc.
>
> Also confirm that the outcome is reproducible by running replicates.  A
> single trajectory is not necessarily definitive of anything.
>
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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