AMBER Archive (2005)

Subject: Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Thu Jun 30 2005 - 02:14:01 CDT

Dear Zhiguo,

calculating bindung free energies between protein molecules is within the
scope of MM-PBSA. This paper describes something similar:

Gohlke H. ; Case D.A. 2003 Converging free energy estimates: MM-PB(GB)SA
studies on the protein-protein complex Ras-Raf J. Comput. Chem. 25,
238-250

The size of the system should be no problem for the MM and PB parts of the
calculation.

You might however run into problems doing nmode calculations on so large a
system, so you proably have to figure out a way to estimate the entropy
contribution to binding, like assuming only the classical rotational and
translational degrees of freedom are lost.

Kind Regards,

Thomas

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