Re: AMBER: absolute vs. relative binding free energy

From: David A. Case <>
Date: Wed, 5 Nov 2003 17:45:54 -0800

On Wed, Nov 05, 2003, Qing Zhang wrote:
> I have two protein/DNA complex systems with a
> carcinogen at two different locations in the DNA. I
> compute the binding free energy (using MM-PBSA method)
> between protein and carcinogen-modified DNA for each
> system, and find the relative binding free energy
> between these two systems are very close to
> experimental result. But the absolute binding free
> energy of each system is around -500 kcal/mol, which
> is far away from experiemental value of around -10
> kcal/mol.

Something is wrong with the calculations. MM-PBSA is far from perfect, but
it should not give nonsensical answers either. It is almost certainly
worthwhile for you to examine all of the pieces of the energy decompostion
carefully, searching for something that is not being done correctly.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Nov 06 2003 - 01:53:01 PST
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