AMBER Archive (2006)

Subject: Re: AMBER: Quantifying pi-pi interactions

From: Jiri Sponer (
Date: Tue Nov 21 2006 - 10:14:32 CST

The only meaningful way is, to may opinion, monitoring of
the Lennard-Jones component of the stacking energy.
This is equivalent to what crystallographers call
"aromatic ring overlap" but much more exact.
(Visual inspection can be easily misleading).
Attempts to rely on some geometrical criteria are often
misleading and cause numerous incorrect statements about molecular
interactions in the literature.
Stacking interactions, in contrast to H-bonding, are not directional
and thus very elusive when some single distance is used for definition.
We have noticed this couple of times, I do not remember where
exactly, perhaps may be here:

Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
Sponer et al.
CHEM EUR J 12 2854 2006

Best wishes

Jiri Sponer
Associate Professor of Biophysics
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 Editor - Journal of Biomolecular Structure and Dynamics,
Adenine Press, NY
Senior Wellcome Trust International Research Fellow for Biomedical Science

> My colleagues and I have been searching and poring over literature for quite
> some time trying to extricate pi-stacking interactions from molecular
> dynamics. We've tried C-C distances in an attempt to find the correlation,
> but it seems as if there should be a better method for finding them.
> Ideally, PTraj would have some sort of aromatic equivalent of the
> easy-to-use (and very informative) hydrogen bonding utility. Unfortunately,
> we haven't been able to quantify our findings (we believe we can SEE the
> pi-stacking when we watch the trajectory movie)
> Can anybody advise us as to which method is most optimal for quantifying
> pi-stacking?
> Thank you very much!
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