Let us suppose that the user wishes to test AutoDock by trying to reproduce an x-ray crystallographic structure of a ligand-enzyme complex taken from the Brookhaven Protein Data Bank. The first step is to split the desired PDB file into two separate PDB files, one containing all the heavy atoms of the enzyme, the other containing those of the ligand. Both files should retain the extension `.pdb'.
Note : Care should be taken when the PDB file contains disordered residues, where alternate location indicators (column 17) have been assigned. For each such atom, the user must select only one of the possible alternate locations (preferably that with the highest occupancy value).
We will discuss in the next sections, the steps needed to prepare the parameter files for AutoGrid and AutoDock. If desired, the user may specify rotatable bonds in the ligand (receptor flexibility is not allowed). To help this definition, there is a program called AutoTors . This utility interactively queries the user about the rigid portion of the molecule (the "root") and rotatable torsions (the "branches" and "torsions"). Then it outputs the ligand in PDBQ format for AutoDock . It can even process partial charges on the hydrogens to create a polar-hydrogen only version of the ligand. This will be discussed in greater detail below.