ADL: pi-pi bond interaction

Oleg Trott trott at scripps.edu
Wed Feb 12 12:02:47 PST 2014


Hi

It's not true that Vina focuses only on polar contacts, but it's true
that it doesn't include any specialized pi-stacking term.

Although it would be *relatively* easy to add to Vina, as I understand
it, the subject is controversial:
http://pubs.rsc.org/en/Content/ArticleLanding/2012/SC/c2sc20045g

On Tue, Feb 11, 2014 at 9:44 AM, Christian Berk <chris.berk at web.de> wrote:
>
>    Dear all,
>
>    I  want  to  dock a substrate into a given crystall structure which is
>    presumably held in place via a pi-pi bond interaction. The results I get
>    back from AutoDock vina appear not to consider a pi-pi bond interaction but
>    rather focus on polar contacts only. Is that correct? Can you recommend a
>    way to perform the docking considering a pi-pi bond interaction?
>
>    Kind regards,
>
>    Christian Berk
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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