AMBER: No vdW parameters for HO..

From: Vineet Pande <>
Date: Fri, 06 May 2005 10:20:02 +0000


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. I am expressing this concern because in explicit
solvent simulations I performed with a kinase, 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!.......Is there any
justification for this?


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Received on Fri May 06 2005 - 11:53:00 PDT
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