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

From: Mahmoud Soliman <>
Date: Mon, 21 Mar 2011 19:40:24 +0200

   Thanks Case for your comment!
   Best wishes
   On 3/21/11 7:23 PM, case wrote:

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.


AMBER mailing list



   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath


   BA2 7AY

   United Kingdom




   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University









AMBER mailing list
Received on Mon Mar 21 2011 - 11:00:02 PDT
Custom Search