AutoDock Version 4.2

Atom types present in the ligand, separated by spaces, such as, “A C HD N NA OA SA”.receptor Macromolecule filename, in PDBQT format.gridcenter gridcenter auto[auto]The user can explicitly define the center of the grid maps, respectively the x, y and z coordinates ofthe center of the grid maps (units: Å, Å, Å.) Or the keyword “auto” can be given, in which caseAutoGrid will center the grid maps on the center of the macromolecule.smooth [0.5 Å]Smoothing parameter for the pairwise atomic affinity potentials (both van der Waals and hydrogenbonds). For AutoDock4, the force field has been optimized for a value of 0.5 Å.map Filename of the grid map for each ligand atom type; the extension is usually “.X.map”, where“X” is the atom type. One line is included for each atom type in the ligand_types command,in the order given in that command.elecmap Filename for the electrostatic potential energy grid map to be created; filename extension ‘.e.map’.dsolvmap Filename for the desolvation potential energy grid map to be created; filename extension ‘.d.map’.dielectric [-0.1465]Dielectric function flag: if negative, AutoGrid will use distance-dependent dielectric of Mehler andSolmajer; if the float is positive, AutoGrid will use this value as the dielectric constant. AutoDock4has been calibrated to use a value of –0.1465.28