[AMBER] scientific question on decomposition analysis in pbsa calculation

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Wed, 23 Mar 2011 16:20:37 +0200

   Dear All,
   In our group we only have Amber 10 installed on the cluster and as I know
   decomposition analysis PBSA calculation can not be done using Amber 10. Let
   me quickly explain to you the piece of work I am trying to investigate using
   Amber. I would like to explore the influence of the nearby active site
   residues on the ligand binding to the enzyme. Mutation of some of these
   residues resulted in a complete loss of the enzyme activity. I was planning
   to run PBSA calculation to see how each residue contributes to the overall
   binding using the decomposition analysis method but I realized that Amber10
   can not achieve this.My question is can I calculate the total binding energy
   for the wild type then do the same thing for a particular mutant, I wonder,
   can that give me an estimate on the contribution of this residue that I have
   mutated to the overall binding .... Your scientific idea are most welcome!!!
   Thanks in advance
   Best wishes



   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath


   BA2 7AY

   United Kingdom




   1. http://people.bath.ac.uk/mess20/
   2. http://www.bath.ac.uk/person/812559
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Received on Wed Mar 23 2011 - 07:30:03 PDT
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