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
--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[1]
http://people.bath.ac.uk/mess20/
[2]
http://www.bath.ac.uk/person/812559
References
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
