DNA base-step distortion

From: <kbyun.wesleyan.edu>
Date: Sun, 18 May 2003 15:37:12 -0400 (EDT)

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

         
Received on Sun May 18 2003 - 20:53:01 PDT
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