[gmx-users] Query of RMSD results

[Sainitin Donakonda]

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.

Thanks,
Sainitin

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
>> on
>> 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
>> you
>> 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
>
> --
> ==================================================
>
> 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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