AMBER Archive (2006)

Subject: AMBER: Quantifying pi-pi interactions

From: zachary hartman (
Date: Tue Nov 21 2006 - 09:51:30 CST

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

Thank you very much!

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