AutoDock Version 4.2

sw_rho [1.0]This is a parameter of the Solis & Wets algorithms. It defines the initial variance, and specifies thesize of the local space to sample.sw_lb_rho [0.01]This is the lower bound on rho, the variance for making changes to genes (i.e. translations, orientationand torsions). rho can never be modified to a value smaller than “sw_lb_rho”.ls_search_freq[0.06]This is the probability of any particular phenotype being subjected to local search.Commands to choose and set the local search methodBoth of these commands, ’set_sw1’ and ’set_psw1’, pass any ’sw_’ parameters set before thisline to the local searcher. If you forget to use this command, or give it before the ’sw_’ keywords,your choices will not take effect, and the default values for the optimizer will be used. Currently, thepsw1 method has shown the best performance and is used as the default.set_sw1Instructs AutoDock to use the classical Solis and Wets local searcher, using the method of uniformvariances for changes in translations, orientations, and torsions.set_psw1Instructs AutoDock to use the pseudo-Solis and Wets local searcher. This method maintains therelative proportions of variances for the translations in Å and the rotations in radians. These aretypically 0.2 Å and 0.087 radians to start with, so the variance for translations will always be about2.3 times larger than that for the rotations (i.e. orientation and torsions).Commands to specify the search methodsimannealThis command instructs AutoDock to do the specifed number of docking runs using the simulatedannealing (SA) search engine. This uses the value set by the “runs” keyword as the number of SAdocking runs to carry out. All relevant parameters for the simulated annealing job must be set first.These are indicated above by [SA] in each keyword description.do_local_only [50]This keyword instructs AutoDock to carry out only the local search of a global-local search; thegenetic algorithm parameters are ignored, with the exception of the population size. This is an idealway of carrying out a minimization using the same force field as is used during a dockingcalculation. The “ga_run” keyword should not be given. The number after the keyworddetermines how many local search simulations will be performed.42