doubt regarding Auto dock

[ADARSH V. K.]

Dear All,

I have certain doubt regarding Auto dock. 1st time I am going to use auto-dock.

1) Before docking a new ligand with auto-dock, is there any requirement to remove co-crystallized ligand form PDB structure ?.
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2) Is there any requirement to specify the active site residues or Auto-dock will find its own and dock ? (In case protein structure with out a co-crystallized ligand)
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3) Is there any other important points to be considered while docking with Auto-dock?

Regards,
Adarsh

[ADARSH V. K.]