explicit hydrogen bonds

From: Matthew Wilce (Matthew.Wilce_at_med.monash.edu.au)
Date: Thu May 11 2006 - 00:54:20 CDT

could you someone shed some light on the use of explicit hydrogen
bonds in namd.
I notice that Klaus Schutlen's 2003 fibronectin paper in PNAS uses
explicit hydrogen bonds.
How does one do this? as they are not part of CHARMM?
In particular, I am working with double stranded DNA which starts to
unwind during a MD simulation. I am hoping to use base pairing
hydrogen bonds to prevent this rather than fixing or restraining
atoms in the dna.
Thanks in advance,

Associate Professor Matthew Wilce
Department of Biochemistry and Molecular Biology
Monash University
Victoria, Australia

Phone: 613 9905 1086

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