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

From: Jiri Sponer <>
Date: Sat, 22 May 2004 16:09:46 +0200 (MEST)

 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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Received on Sat May 22 2004 - 15:53:01 PDT
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