If I specify “do_local_only” in the DPF, what exactly is being energy-minimised?
Whatever you have specified as flexible will be energy minimised: at least the ligand, and if you have any, the flexible sidechains you have specified with the “flexres” keyword in the DPF. The energy minimisation will be performed in the context of the grid maps you have calculated for the receptor. So you could use this command to optimise the position, orientation and conformation of a ligand in an active site, to remove any bad contacts that may be present in an x-ray crystal structure. The ligand’s position, orientation and torsion angles (if flexible) will be optimised, in addition to any flexible sidechains’ torsion angles if specified. The starting point of the ligand can be controlled by the “tran0”, “quaternion0” and “dihe0” keywords in the AutoDock 4 DPF. (Note that in AutoDock 3, the orientation is specified using the “quat0” keyword.) • To keep the ligand’s input position the same as in the ligand PDBQT, use the same “tran0” x,y,z values as those specified in the “about” l
