AMBER Archive (2000)

Subject: Re: estimate entropy of dna using nmode

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Mar 17 2000 - 12:05:39 CST

> 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