The best way to get started with docking is to follow the detailed tutorial in our Nature Protocols paper:
Computational Ligand-Protein Docking and Virtual Drug Screening with the AutoDock Suite.
It is freely available on PubMedCentral, and also available in nice formatted form through Nature Protocols. Be sure to download the supplementary files, which include several worked examples that you can try out.
The AutoDock4.2.6_UserGuide includes full description of the functionality of AutoDock4.2 and AutoGrid4.2. For more information and other resources, visit the Documentation page.
ADL, the AutoDock Mailing List, is intended for novice and expert users of the ligand-protein and protein-protein docking software suite of AutoDock, AutoGrid and AutoDockTools (ADT). It brings together a community of people that have common interests in molecular modeling software related to docking and AutoDock, and are here for learning or helping others. It is also a forum for suggesting new features, and new software versions and functionality will be announced on the list.