AMBER Archive (2004)

Subject: Re: Re: Re: AMBER: a question about Van der waals radius

From: Xiao He (
Date: Sat May 22 2004 - 09:29:56 CDT

  I use DFT and also HF,too.There exits the repulsive reaction between them,
while force field can not show this repulsive reaction.
  I just calculate the binding energy between protein and drug.
  I'm going to do a systemic study on this to show the E = E(R) profile.
I just wanna to ask whether it may be a problem of Amber force field
according to other users' experience, and whether it is a good project
otherwise it will waste my time.
  Thank for anyone's suggestion.

He Xiao

> In my calculation of the interaction energy between a CYS residue of protein
> and ligand of Nevirapine a HIV-1 RT drug). Since the van der waals radius
> of the H linked to the S atom is 0.6A.While the distance between this H atom
> with carbon atom in Nevirapine is 1.93A.
> The interaction energy is incompatible with the ab initio Gaussian result.
> There's a strong repulsive reaction energy about 9 Kcal/mol using B3LYP/6-31G(d).
> While using Amber7 it is around zero.
> Can we say it is a failure of force field?And the van der waals radius may be
> a bit modified.
> Thanks for anyone's help!
> He Xiao
>Dear He Xiao
>It is not easy to decide as DFT is not necessarily correct
>for intermolecular forces (dispersion energy is completely neglected).
>So if there is anything stacking-like DFT is of no use.
>However, it may well be force field imbalance.
>Do you refer to X-ray, MD or ab initio optimized geometry?
>Try to calculate few points for different intermonomer distances,
>i.e., the E = E(R) profile. Then one can see whether the problem originates
>from the short-range repulsion or something else.
>best wishes,
>Jiri Sponer
>Jiri Sponer
>Institute of Biophysics
>Academy of Sciences of the Czech Republic
>Kralovopolska 135
>CZ-61265 Brno
>Czech Republic
>fax: 420 5412 12179
>phone: 420 5415 17133
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        Xiao He

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