AMBER Archive (2005)

Subject: Re: AMBER: No vdW parameters for HO..

From: Yong Duan (duan_at_albert.genomecenter.ucdavis.edu)
Date: Fri May 06 2005 - 11:28:25 CDT

> when the Hbond is buried), and we see that Electrostatic term of binding
> energy shoots more negative, while vdW energies are positive, ...perhaps due
> to heavy atoms getting close enough....so I was saying "artifactual" to a

The vdW terms is expected to become positive for H-bond pairs which is
part of the check and balance. Nevertheless, you are correct that the zero
vdW term of HO can make HO:X h-bonds closer. This is one of the issues
that need to be addressed in ff. Unfortunately, it is seriously tangled up
with other issues like solvent models which are already difficult issues
by themselves.

yong

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