ADL: regarding active site

Oleg Trott trott at
Sat Jun 13 11:35:41 PDT 2009

On Fri, Jun 12, 2009 at 3:53 PM, Davide
Mercadante<dmer018 at> wrote:

> 2) After the calculations the docked ligands are not in the box that I built
> to perform the calculation

Are you using AutoDock 4 or AutoDock Vina? In Vina, there is a stiff
scoring function penalty for going outside the box, so the ligand is
very unlikely to stray too far.

Oleg Trott, Ph.D. (Columbia University)

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