Re: [AMBER] can I calculate binding energy with some restraints

From: case <>
Date: Mon, 21 Mar 2011 13:23:35 -0400

On Mon, Mar 21, 2011, Mahmoud Soliman wrote:
> I need to calculate the binding energy for some synthesized ligands in our
> lap with some artificial enzyme (which I simulate as well). the problem is
> that I notice these ligands does not stick to the protein (as it appear in
> X-ray structure that we developed also in our lap) in a free MD simulation.

You won't be able to estimate the binding energies if the bound complex is not
stable in an MD simulation. You *might* use restraints to force binding, and
study resultant snapshots for clues as to why the ligand is not happy in the
binding site.


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Received on Mon Mar 21 2011 - 10:30:04 PDT
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