AMBER Archive (2003)

Subject: DNA base-step distortion

From: kbyun_at_wesleyan.edu
Date: Sun May 18 2003 - 14:37:12 CDT

Hi,
I'm using MD to study the structure of two protein-dna
complexes. I'm including explicit solvent and
counter-ions. The difference between the two complexes
comes from part of the DNA sequence. For one complex,
the basestep parameters roll and tilt differs
considerably with the starting crystal structure, and I
suspect this is coming from the force field. For the
second complex, MD reproduces the crystal structure
quite well. Is it common to see differences like this?
 I was wondering if people could offer some pointers on
how I can solve the discrepancy.

Thanks very much,

Suzie Byun