On Fri, Feb 01, 2013, Date, Mihir wrote:
> I want to calculate protein-protein binding free energy of a
> homo-dimer. I have the simulations run for it using Amber 12. It does
> not have any ligand present. While looking at mmpbsa_pl or mmpbsa_py it
> seems both of the documentations and examples illustrates calculation of
> binding free energy for protein-ligand system which includes specifying
> protein and ligand topology file separately. Can anybody point me
> towards the examples of calculating protein-protein binding free energy?
> or the changes I have to make to use protein-ligand mmpbsa scripts for
> protein-protein system?
The "ligand" could be another protein. You might want to look at the papers
below for an (old) discussion of the prospects and pitfalls of such
calculations:
%A H. Gohlke
%A C. Kiel
%A D.A. Case
%T Insights into Protein-Protein Binding by Binding Free Energy Calculation
and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes
%J J. Mol. Biol.
%V 330
%P 891-913
%D 2003
%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004
....dac
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Received on Fri Feb 01 2013 - 19:00:03 PST
