AMBER Archive (2000)

Subject: Re: estimate entropy of dna using nmode

From: David Case (case_at_scripps.edu)
Date: Fri Mar 17 2000 - 10:21:15 CST


On Thu, Mar 16, 2000, Frank Yan wrote:

> we're using nmode to estimate the entropy of a dna sequence with a
> carcinogen binded. we took out the structure from dynamics trajectory, then
> do minimization exclude water and ions but using a 4r dd to mimic solvent.
> we found that after minimization using a drms of 0.0001 the structure is
> extremely distorted to a kind of denatured state...

You are seeing a big problem (perhaps an Achilles heel?) of the mm_pbsa
approach: there are no really good ways to estimate entropy changes for
many interesting types of transformations. This is still a very active
area of research.

If you want to use normal modes, you have to go to a very small gradient
in order to get useful results. Otherwise, you will have "imaginary"
frequencies whose contributions to fluctuations is not well-defined.

...good luck....dac

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | WWW: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================