AutoDock Version 4.2

AutoDock Docking Parameter File: DPFExtension: .dpfThe docking parameter file specifies the files and parameters for an AutoDock calculation,including the map files that will be used for the docking, the ligand coordinate files, and parametersfor the search. Unlike previous versions of AutoDock, the pairwise atomic parameters used for theinternal energy calculation may now read from a separate file (described above), or taken fromdefaults in AutoDock.All delimiters where needed are white spaces. Default values assigned by AutoDockTools, whereapplicable, are given here in square brackets [thus]. A comment must be prefixed by the “ # ”symbol, and can be placed at the end of a parameter line, or on a line of its own. Although ideally itshould be possible to give these keywords in any order, not every possible combination has beentested, so it would be wise to stick to the following order.Parameter to set the amount of outputoutlev [1]Diagnostic output level. For SA (simulated annealing): 0 = no output, 1 = minimal output, 2 = fullstate output at end of each cycle; 3 = detailed output for each step. For GA and GA-LS (geneticalgorithm-local search): 0 = minimal output, 1 = write minimum, mean, and maximum of each statevariable at the end of every generation, 2 = full output at every generation.Atomic parameters for pairwise energy evaluationparameter_file (Optional) Atomic parameter file used for pairwise energy evaluation in internal energies andinteractions between ligand and flexible sidechains. If this is not given, AutoDock uses defaultparameters identical to values in the file AD4.2_bound.dat.intelec(Optional) If this keyword is included, internal ligand electrostatic energies will be calculated; theproducts of the partial charges in each non-bonded atom pair are pre-calculated, and output. Notethat this is only relevant for flexible ligands.intnbp_r_eps (Optional) This optional keyword allows the user to manually override the internal energy potentialfor a given class of interactions. The parameters are: r eq, ε, n, m, and the two atom types, where r eqisthe equilibribium distance for the bottom of the energetic well, ε is the depth of the well, n and m arethe coefficients. For instance, the command “intnbp_r_eps 1.5 10. 12 6 OA FE” will set up apotential with well depth of 10 kcal/mol at a distance of 1.5 Å for interaction between oxygen andiron atoms. The potential V(r) is calculated with the expression:V(r)=C n/r n – C m/r mC n= m/(n-m) * ε *r eqn33