AutoDock requires pre-calculated grid maps, one for each atom type present in the ligand being docked. These maps are calculated by AutoGrid. A grid map consists of a three dimensional lattice of regularly spaced points, surrounding (either entirely or partly) and centered on some region of interest of the macromolecule under study. This could be a protein, enzyme, antibody, DNA, RNA or even a polymer or ionic crystal. Typical grid point spacing varies from 0.2Å to 1.0Å. Each point within the grid map stores the potential energy experienced by a ` probe ' atom or functional group due to all the atoms in the macromolecule.
The user must specify an even number of grid points in each dimension, n x , n y and n z . This is because AutoGrid adds a central point, and AutoDock requires an odd number of grid points. The probe's energy at each grid point is determined by the set of parameters supplied for that particular atom type, and is the summation over all atoms of the macromolecule, within a non-bonded radius, of all pairwise interactions.
The following figure illustrates the main features of a grid map:
The ligand can be seen in the centre of the grid map, buried inside the active site of the protein. In this case, the grid map encompasses the whole protein. The grid spacing is the same in all three dimensions.