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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Received on Wed Nov 22 2006 - 06:07:36 PST
