AutoDock Version 4.2

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schedules in simulated annealing and mutation/crossover rates in genetic algorithms. For details ofeach parameter, see the full description in the Appendix.Docking>DockingParameters: opens a panel for setting the parameters used during thedocking calculation, including options for the random number generator, options for the force field,step sizes taken when generating new conformations, and output options. For details of eachparameter, see the full description in the Appendix I.Docking>OtherOptions: specifies the name of an external atomic parameter file, if used.Docking>OutPut>LamarckianGA:Docking>OutPut>GeneticAlgorithm:Docking>OutPut>SimulatedAnnealing:Docking>Output>LocalSearch: These four commands write the docking parameter fileusing one of the four available search methods.Docking>Edit: interactive editor for docking parameter files, which allows viewing of the lastestdocking parameter file written by AutoDockTools.20
STEP 4: Evaluating the Results of a DockingAt the end of a docking simulation, AutoDock writes the coordinates for each docked conformationto the docking log file, along with information on clustering and interaction energies.AutoDockTools provides options for analyzing the information stored in the docking log file.Information in the Docking LogThe analysis command in the docking parameter file causes AutoDock to perform a clusteranalysis of the different docked conformations. The results of this analysis are reported as ahistogram, which may be found by searching for the word “HISTOGRAM” (all in capital letters)in the docking log file. This is followed by a table of RMSD values within each cluster.AutoDock then writes coordinates for the conformation of best predicted energy in each cluster (towrite coordinates for all conformations, include the keyword write_all in the docking parameterfile). A header for each conformation includes information on the predicted energy of binding,broken down into several components, along with information on the state variables of theconformation. The coordinates are written in a modified PDB format, with four real valuesappended after the x,y,z coordinates: the vdW+hbond energy of interaction of the atom, theelectrostatic interaction of the atom, the partial charge, and the RMSD from the referenceconformation.Analyzing Docking Results with AutoDockToolsOptions in the “Analyze” menu of AutoDockTools may be used to process and analyze the resultsfrom a docking simulation.Analyze>Dockings>Open: opens a docking log file.Analyze>Dockings>OpenAll: opens a set of docking log files in a directory.Analyze>Dockings>Select: selects from a set of log files previously read intoAutoDockTools.Analyze>Dockings>Clear: clears log files that have been read into AutoDockTools.Analyze>Dockings>ShowAsSpheres: creates a sphere at the center of mass of each dockedconformation, which may be colored according to the predicted energy of interaction.Analyze>Dockings>ShowInteractions: creates a specialized visualization to highlightinteractions between the docked conformation of the ligand and the receptor. By default, the ligandis shown as ball-and-stick, surrounded by a molecular surface. The surface is colored with atomiccolors in regions that contact the receptor, and gray in regions that are not in contact. Portions of thereceptor that are in contact with the ligand are shown with ball-and-stick and spacefilling spheres.Hydrogen bonds are shown as a string of small spheres. A dialogue box is also launched thatprovides many other options for visualization.21
Page 5 and 6: Expanded Atom Types. Parameters hav
Page 7 and 8: TheoryOverview of the Free Energy F
Page 9 and 10: AutoDock Potentials. Examples of th
Page 11 and 12: Care should be taken when the PDB f
Page 13 and 14: Edit>Delete: several options for de
Page 15 and 16: STEP 2: Running AutoGridAutoDock re
Page 17 and 18: STEP 3: Docking with AutoDockAutoDo
Page 19: “unbound_model_extended.” This
Page 23 and 24: Clusterings>Recluster: Reclusters d
Page 25 and 26: Sample PDBQT fileREMARK 4 active to
Page 27 and 28: AutoGrid Grid Parameter File: GPFEx
Page 29 and 30: Atomic Parameter FileFilename: AD4.
Page 31 and 32: Grid Map FileExtension: .mapThe fir
Page 33 and 34: AutoDock Docking Parameter File: DP
Page 35 and 36: Filename for the electrostatics gri
Page 37 and 38: falls within a disallowed zone, how
Page 39 and 40: is small enough to fit into the low
Page 41 and 42: [10]This is the number of preceding
Page 43 and 44: do_global_only [50]This keyword ins
Page 45 and 46: Ring closure parameters. Comparison
Page 47 and 48: implicit limit of the docking compl
Page 49: Appendix III: AutoDock ReferencesAu

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