[gmx-users] Interaction energy graph

[Justin Lemkul]

On 3/16/14, 12:49 AM, kannan wrote:
> Dear Justin,
> sorry sir i forget to attahc the files, it is here attached. Thank you very
> much for your reply.. I answer the above question,
> 1. I am doing the protein-ligand interaction(electrostati+vanderWaals). I
> took the 140 amino acid as a sequence which contains binding site of the
> protein in Chain A of protein.
> 2. why i choose this sequence is, to know the binding interaction in deep.
> my objective is what are the amino acid residues are important for the
> interaction with ligand and if we dock the ligand far away from the
> important amino acid residues(which is essential for strong binding), how
> the interaction energy varies.
> 3. while docking ligand with important amino acid residue, i get the
> 'A-plot', where as if i dock the ligand far away from this particular amino
> acid residue, i get the 'B-plot'.
>
> I think, my conclusion is that, the decreasing interaction in the B-plot is
> due to the lack of the particular one important amino acid residue. so this
> particular residue and its region is has more contribution in the binding...
>
> I attached both the A-plot and B-plot sir...
>
> is my conclusion correct from the graph?
>

The function of this mailing list is for getting help with Gromacs problems, not 
doing your data interpretation for you.  Consult with your supervisor and/or 
colleagues, who know more about your project and problem at hand than any of us 
can possibly hope to.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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