ADL: regarding active site

Bagdevi bagdevi.mishra at
Sat Jun 13 13:14:12 PDT 2009


I assume you are using autodock4. Just check and be sure of the grid
size, it should just cover the active site, it should not go beyond
the protein size. The algorithm does not allow the movement of the
ligand out of the grid box. If your grid just covers the active site,
it will calculate the binding energies, at different positions inside
the active site only. When you visualize the results, if you see the
ligand is far away from the active site, that means your grid is big
enough, which you need to change and in case you are sure that you
have build the appropriate grid box, may be you are loading the wrong
conformation of the ligand while visualizing it after docking.

Bagdevi Mishra.

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