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- AutoGrid is a program that pre-calculates grid maps of interaction energies for various atom types, such as aliphatic carbons, aromatic carbons, hydrogen bonding oxygens, and so on, with a macromolecule such as a protein, DNA or RNA. These grid maps are then used by AutoDock docking calculations to determine the total interaction energy for a ligand with a macromolecule. Doing this pre-calculation saves a lot of time during the docking, primarily because we do not have to update non-bonded lists during the calculation. Also, what was a calculation with order N-squared complexity, is reduced to one that is order N, where N is the number of atoms interacting.
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AutoDock Vina now has an FAQ