AMBER Archive (2003)

Subject: AMBER: absolute vs. relative binding free energy

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Wed Nov 05 2003 - 18:24:45 CST

Dear Amber users:

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.

Some literature does get absolute binding free
energies close to experimental values. Others not. Is
there any story behind this? Is that because force
field, or something else?

Thanks,

Qing Zhang

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