Re: explicit hydrogen bonds

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Thu May 11 2006 - 10:41:56 CDT

Mathew,
While I haven't read Schulten's 2003 PNAS paper, I do recall another
paper on the Ig titin domains: Lu and Schulten 2000 Biophys. J.
79:51-65. In the last paragraph of the method section they explain that
the simulations were run using the CHARMM22 force field, where the
hydrogen bonding interactions are implicit in the force-field. However,
they analyzed the trajectories using the XPLOR program, which does have
an explicit hydrogen bonding enegy term. In my opinion, this means that
the hydrogen bond energies they report can only be used as a qualitative
measure of the hydrogen bond interactions. I would assume that they did
the same for the 2003 PNAS paper.

I don't know why your DNA strand is unwinding. How big is it, how long
does it take to unwind, and are you using explicit solvent?

-Sterling

Matthew Wilce wrote:

> Hi,
> 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,
> Matt
> *
> *
> *Associate Professor Matthew Wilce*
> Department of Biochemistry and Molecular Biology
> Monash University
> Victoria, Australia
>
> Phone: 613 9905 1086
>
>
>

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