[gmx-users] Query of RMSD results

[Justin Lemkul]

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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