[gmx-users] Interaction energy graph

[kannan]

Dear Justin,
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?

Thank you justin
kannan s



On Sat, Mar 15, 2014 at 7:15 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5015170h17 at n6.nabble.com> wrote:

>
>
> On 3/15/14, 2:17 AM, Kannan S wrote:
> > Dear Gromacs users,
> > i run dynamics for 20 ns and plot the interaction energy which i
> attached
> > with this..
> >
>
> Attachments aren't allowed on the list.  Link to a file if you want to
> share it.
>
> > is this plot correct?
> >
>
> No one here can know this.  We don't know what the interaction energy is,
> or why
> you measured it, so "correct" is up to you and your knowledge of what you
> are
> doing.  If you need help understanding how to correctly obtain interaction
> energies between species in the system, you need to tell us:
>
> 1. What you are studying
> 2. What your objective is
> 3. What you have tried to do to accomplish #2
>
> -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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