Dear Mahmoud,
Is there any reason that you cannot install the latest free AmberTool
release? Also, are you using the mmpbsa perl script for this? Can you run
the example?
All the best,
Ray
On Wed, Mar 23, 2011 at 7:20 AM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 23 2011 - 07:30:05 PDT
