HOW TO USE
Installation
  1. Download and uncompress the content of the compressed file in one directory.
  2. Enter into the autodock folder

    %> cd autodock
  3. If you are using Linux or Mac OSX, you shouldn't have any problems to compile the code. If you are using Windows, you would need to use Cygwin to compile the code.
    Enter the following lines in your terminal window:

    %> ./configure
    %> make
How to execute jMetal algorithms

This version of AutoDock with jMetalCpp is used like the original version of AutoDock. You only need to edit your Docking Parameter File (DPF) to include some extra parameters needed to configure jMetal.

  1. You need to include two extra parameters into your DPF:

    • jmetal_alg <jMetal_algorithm>
    • jmetal_run <number_of_executions>


    The possible values that you can specify in <jMetal_algorithm> are:

    • Mono-objective: gGA, ssGA, DE or PSO
    • Multi-objective: NSGAII, ssNSGAII, SMPSO, GDE3, MOEAD, SMSEMOA


    IMPORTANT: jMetal algorithms needs two already existing DPF parameters ga_num_evals (number of evaluations) and ga_pop_size (population size).

    For example, the content of one possible DPF in which we have specified to use the DE (Differential Evolution) algorithm and a number of 100 executions is the following:
    autodock_parameter_version 4.2 # used by autodock to validate parameter set outlev 1 # diagnostic output level intelec # calculate internal electrostatics seed pid time # seeds for random generator ligand_types A NA C OA N # atoms types in ligand fld macro.maps.fld # grid_data_file map macro.A.map # atom-specific affinity map map macro.NA.map # atom-specific affinity map map macro.C.map # atom-specific affinity map map macro.OA.map # atom-specific affinity map map macro.N.map # atom-specific affinity map elecmap macro.e.map # electrostatics map desolvmap macro.d.map # desolvation map move Indinavir0.pdbqt # small molecule about 14.7956 19.5682 6.4938 # small molecule center tran0 random # initial coordinates/A or random axisangle0 random # initial orientation dihe0 random # initial dihedrals (relative) or random tstep 2.0 # translation step/A qstep 50.0 # quaternion step/deg dstep 50.0 # torsion step/deg torsdof 12 # torsional degrees of freedom rmstol 2.0 # cluster_tolerance/A extnrg 1000.0 # external grid energy e0max 0.0 10000 # max initial energy; max number of retries ga_pop_size 150 # number of individuals in population ga_num_evals 1500000 # maximum number of energy evaluations ga_num_generations 27000 # maximum number of generations ga_elitism 1 # number of top individuals to survive to next # generation ga_mutation_rate 0.02 # rate of gene mutation ga_crossover_rate 0.8 # rate of crossover ga_window_size 10 # ga_cauchy_alpha 0.0 # Alpha parameter of Cauchy distribution ga_cauchy_beta 1.0 # Beta parameter Cauchy distribution set_ga # set the above parameters for GA or LGA unbound_model bound # state of unbound ligand jmetal_alg gGA # choose this jMetal algorithm jmetal_run 100 # do this many jMetal runs
  2. Execute the program as you normally execute AutoDock:

    %> ./autodock4 -p <docking_parameter_file> -l <docking_log_file>

    The generated Docking Log File (DLG) will include one solution for each run (when executing a mono-objective algorithm) or multiple solutions for each run (when executing a multi-objective solution).
Introduction |  Download |  How to use |  Instances |  People |  Acknowledgements