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

From: Thomas Steinbrecher <>
Date: Thu, 30 Jun 2005 00:14:01 -0700

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,

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

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,


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Received on Thu Jun 30 2005 - 08:53:00 PDT
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