[AMBER] which methods calculate the binding energy most accurate

From: Acoot Brett <acootbrett.yahoo.com>
Date: Wed, 11 Apr 2012 18:21:14 -0700 (PDT)

Dear All,
There is a series of protein-peptide dimer, in the dimers all the protein are the same protein, with about 400 aas. In the dimer, the peptide can be any one of a series of highly consered peptides with about 15 aas.
There is difficulty to get accurately the binding energy between the protein and the peptide. Or the binding energy could be got, but caused by the assay method the measured binding energy differnece among different dimers cannot be explained by the correspdonding dimer 3-D structural difference.
I plan to use AMBER to calculate the binding energy between the peptide and the protein in each dimer.
Will you please give me some comment on the available AMBER calculation methods, corresponding calculation accuracy and the corresponding calculation time length for the calculation of the binding energy?
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Received on Wed Apr 11 2012 - 18:30:04 PDT
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