AMBER Archive (2007)

Subject: Re: AMBER: Regarding free energy calculation and covalent bond

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 23 2007 - 11:52:17 CDT

On Mon, Aug 20, 2007, nag raj wrote:

> I want to calculate free energy of binding between DNA and ligand. But
> ligand forms covalent bond with DNA. Here I am giving general equation of my
> system (DNA and ligand) forming covalent bond complex.
> (DNA)G-NH2 + R-C=N-R1 (ligand) -----> G-NH-CRH-NH-R1 (complex) >
> My question is how to calculate free energy of complex?

This is a very difficult problem. Molecular mechanics is not equipped to
describe covalent bond formation. You might be able to do a calculation in
the presence and absence of DNA, and learn something from the differences.

There is more work in this field on proteins than for DNA, so you might look
for papers that study the effects of proteins on reaction energetics. Plan on
spending a lot of time learning the basics before attacking the problem listed
above.

...good luck...dac

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