Re: estimate entropy of dna using nmode

From: Bill Ross <>
Date: Fri 17 Mar 2000 10:05:39 -0800 (PST)

> 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...

Possibly there are initial strains that a more careful
minimization would 'solve' without undue distortion.

For example, you could gradually cool the system with
the water and ions before extracting the dna, and/or
start the vacuum minimization by using dynamics at 1-10K,
and/or keep the ions but change their parameters to IB
('fat', pseudo-hydrated ions for vacuum use).

Bill Ross
Received on Fri Mar 17 2000 - 10:05:39 PST
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