[gmx-users] Interaction energy graph

[kannan]

Dear Justin,
Thank you very much for the reply...
I do as you said...

Best regards
kannan s


On Sun, Mar 16, 2014 at 7:54 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5015198h85 at n6.nabble.com> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
>
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