protein/DNA complexes

From: Matthew Wilce (
Date: Fri May 06 2005 - 00:27:34 CDT

I am using namd to simulate the dynamics of hydrogen bonding between
DNA and proteins. I am finding that in some of my simulations some of
the bases of the DNA are dissociating from the protein.

Could anyone with experience in simulating protein DNA complexes offer
an suggestions?

I am particularly interested in the parameters I should use eg.
Switchdist (10.0) and pairlistdist (13.5) etc. Should I be using larger
values due to the DNA?

I am using PME and PBC.

I have found that solvent padding of greater than 7 angstrom is
required to maintain a reasonable RMSD through the simulation.

I have also changed the salt concentration from 0.05 to 0.15 molar and
find that I don't have as many hydrogen bonds maintained at the higher
salt concentration. Is this expected?

any comments appreciated.


Associate Professor Matthew CJ Wilce
Department of Biochemistry and Molecular Biology
School of Medicine, Nursing and Health Sciences
Monash University
Clayton, Wellington Road
Victoria, 3800

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