Targeted? tell me about your target please.

Do you want to dock your ligands to your protein or do you want to find the binding sites? Tell me in detail, please.

I have the coordinates of the ligand binding site. I want to know how to specify that while preparing the Grid file. That's what I meant by targeted Docking.

Thanks in advance.

You can use autodock vina in that you can specify the cordinates (x, y & z) in the configuration file.

Thanks Danish! I initially used AutoDock vina. Recently I got to learn AutoDock Tools. So I was wondering how to do that in ADT. I took the coordinates as the Center of the Grid box and then I did Docking. I compared the Binding affinity values that AutoDock Vina and ADT gave. I was expecting an almost similar value. But to my surprise, ADT gave a value less by 2 Kcal/mol.

Be careful the Scoring functions (delta G etc) are NOT directly comparable between docking programs.

Can you give a few more details (small molecule or peptide ligand, known ligand or screening, etc.)?

If you are interested in sampling one or more small molecules against predetermined locations on known (or previously generated) structures. Dock From UCSF; AutoDock or Vina both from Scripts. Are excellent commonly used free tools.

For the simple cases just use the one you are comfortable with--

ADT (AutoDockTools) is a preparatory and analysis suite for AutoDock and Vina (mostly AutoDock).

These three and many others both commercial and free (and many online) are quite decent at modeling completely rigid and mobile side-chain to small molecule interactions-- but you comparisons of results is limited! Even small adjustments of parameters (ex box size in Vina) matter.  Scoring is semi-arbitrary and parameter dependent.

As a general rule of thumb, the core group is a parameter fixed run (with exhaustive searching if practical),  and what you can compare is approximate pose (

Okay. Thank you so much, Jacob!