Re: AMBER: No vdW parameters for HO..

From: Vineet Pande <>
Date: Fri, 06 May 2005 15:40:09 +0000

> > hydrogen bonds in buried
> > part of protein matrix turned out to be very strong, more than usual and
> > 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
> > 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
>decide whether you are seeing unexpected behavior or not.
Thanks Prof. Case:
Since I used a crystal structure, where an inhibitor is bound to the active
site and the hydrogen bond there is reasonable, the binding energy
component (from ANAL) for the van der waals term is reasonable (p.s. that
these energies are after simple refinement); but then when we perform MD in
explicit solvent, these Hbonds come much closer (thats where i think that
since H does not have any vdw radii, the two heavy atoms tend to come close
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 I was saying "artifactual" to a
comparison of energies and structure to an xtal structure compared against
an MD simulated (infact annealed) structure...
I also noted that when we provide vdW parameters to these hydrogens, the
hydrogen bonds are "not so strong"...

Kind Regards

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Received on Fri May 06 2005 - 16:53:01 PDT
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