A Program for the Automated Docking of Flexible Ligands to Macromolecules.

AutoDock contains the programs
addsol                Program to add solvation parameters to macromolecule ".pdbq" file;
atmtobnd           Program to convert ".atm" atom files to ".bnd" bond files;
autodock           Automated docking of small molecules to proteins, version 3.0;
autogrid            Calculates atomic affinity and electrostatic potential grid maps for use in AutoDock 3.0;
autotors            Interactively defines rotatable bonds in the ligand and creates a ligand PDBQ file for AutoDock.
makelaunch      Program to create scripts to launch concurrent dockings,group results, and create a clustering docking parameter
                            file for AutoDock;
protonate          A utility to add polar hydrogens to proteins.

To use AutoDock in the CSB Core
type setup autodock (or source /srv/local/setup/autodock.set)

Online manual is available for the program. Or you can view the PDF version of the manual. A hardcopy of the manual is available in the CSB Core.
The homepage for the program has more details and helpful links.
Worked examples for the programs can be found in /srv/local/autodock/examples/

AutoDock Tools are installed in the core. Follow the link for instructions on how to use the programs.