Re: estimate entropy of dna using nmode

From: David Case <>
Date: Fri 17 Mar 2000 08:21:15 -0800

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:
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            |
Received on Fri Mar 17 2000 - 08:21:15 PST
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