AMBER Archive (2004)

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

From: Jiri Sponer (
Date: Sat May 22 2004 - 09:42:27 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

I would need to know the van der Waals overlap in your system.
Neither DFT nor HF should be used for systems with dispersion
such as stacking, intercalation, etc.. They fail completely.
cf. for example.
Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
Hobza P, Sponer J
Chemical Reviews
99, 3247-3276, 1999
Base stacking in cytosine dimer. A comparison of correlated ab initio
calculations with three empirical potential models and density functional theory calculations
Sponer J, Leszczynski J, Hobza P
J. Comput. Chem.
17, 841-850 1996

If this is a pure H-bonding than the force field result would
be strange, but I have never seen a failure of this kind for AMBER.
It would be worth to analyze. What is the Lennard Jones component
of your AMBER interaction energy?

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
Senior Wellcome Trust International Research Fellow for Biomedical Science

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