ADL: regarding active site

Kukol, Andreas a.kukol at
Fri Jun 12 03:53:45 PDT 2009

Use AutoDock Tools to centre the grid at a certain protein (receptor) atom in the binding site and then adjust the position of the gridbox manually, such that the centre is centered above the binding site. This works very well, but you need to do it visually.



> -----Original Message-----
> From: autodock-bounces at [mailto:autodock-bounces at] On
> Behalf Of kaustubh
> Sent: 12 June 2009 11:09
> To: autodock at
> Subject: ADL: regarding active site
> How do we specify a known active site.
> The grid generation does not help doing so.
> While I specify to generate grid at the ligand position, it is generated
> some where at vague position and also the docking take place some where
> else, normally at the surface of the protein.
> This is not working out which ever way I try.
> Anybody their to help?
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