Dear Mihir,
You can look in amber advanced tutorial 3 for an example of
"protein-protein" binding free energy calculations and then try to set up
your own protein systems accordingly keeping mind the papers suggested by
Prof. D. Case.
Hope this helps.
http://ambermd.org/tutorials/advanced/tutorial3/
On Sat, Feb 2, 2013 at 8:10 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Sat Feb 02 2013 - 21:30:02 PST
