With the release of AutoDockTools, also known as 'ADT', AutoDock has become more self-sufficient than ever. ADT provides a graphical user interface to set up the ligand PDBQ file, the AutoGrid grid maps, the AutoDock docking parameters, the ability to launch docking jobs, and the ability to read in and analyse DLG AutoDock docking log files. You can visualize isocontoured AutoGrid maps for atomic affinity and electrostatice potential, and compute and display molecular surfaces.

Babel has been ported into ADT, so its Gasteiger partial atomic charge calculation method is available for small molecules, and there is also the ability to assign Kollman united-atom charges to proteins. Previously, you would have needed SYBYL to do this.

You can also assign solvation parameters to a macromolecule, and perform operations like adding hydrogens and merging non-polar hydrogens, or detecting aromatic carbons (necessary for solvation parameters).

ADT is free for non-commercial applications, and is available from Art Olson's Molecular Graphics Laboratory web site.

Take a look at the paper in the Journal of Computational Chemistry comparing Simulated Annealing, Genetic Algorithm and Lamarckian Genetic Algorithm in AutoDock 3.0:

Morris, G. M.,Á Goodsell, D. S.,Á Halliday, R.S.,Á Huey, R.,Á Hart, W. E.,Á Belew, R. K.Á andÁ Olson, A. J.Á (1998), J. Computational Chemistry, 19: 1639-1662.
"Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function".