Re: AMBER: No vdW parameters for HO..

From: David A. Case <>
Date: Fri, 6 May 2005 07:38:16 -0700

On Fri, May 06, 2005, Vineet Pande wrote:
> A question about paramters for hydrogens .....Why do we not have any vdW
> parameters for HO....In the older force fields we did have a parameter for
> this kind of hydrogen.

My best understanding is that the credit/blame for this choice belongs mostly
to Bill Jorgensen and coworkers, who principally did Monte Carlo simulations
on rigid molecules. Setting the H atom vdW parameters to zero meant there was
one less parameter to optimize, and saved some time on pre-historic computers.
It is recommended that you use SHAKE to prevent the OH bond length from

> hydrogen bonds in buried
> part of protein matrix turned out to be very strong, more than usual and I
> attribute this to having no vdW parameters for HO, which brings the two
> heavy atoms where HO is attached to a donor, very close....this leads to a
> very strong electrostatic interaction energy term, but at times an
> artifactual positive vdW interaction energy term!.

Of course, what is "artifactual" is in the eye of the beholder. Without
knowing what you mean by "very strong" and "very close", it is not possible to
decide whether you are seeing unexpected behavior or not.


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Received on Fri May 06 2005 - 15:53:00 PDT
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