Here is my suggestion: If you are working on a protein then the first step woulf be to scan for potential binding surface(which will be defined by the structure of your protein) using something like Peptimap or Pocketquery. After finalizing the binding surface import your surface to ZINCPharmer or Anchorquery. There are many other tools also to do the same and this is just one suggestion. Also most files(masking/screened files) of one server is accomodated in the other making things easier.

Autodock