AutoDock Version 4.2

More documents

Recommendations

Info

$Small-Angle X-ray Scattering SAXS vs. X-ray Diffraction SAXS vs. X ...$

trnrf [1.0]Per-cycle reduction factor for translation steps.quarf [1.0]Per-cycle reduction factor for orientation steps.dihrf Per-cycle reduction factor for torsional dihedral steps [1.].Parameters for genetic algorithm, Lamarckian GA and evolutionary programmingsearchesga_pop_size [150]This is the number of individuals in the population. Each individual is a coupling of a genotype andits associated phenotype. Typical values range from 50 to 200.ga_num_evals [2500000]This is the maximum number of energy evaluations performed during each GA calculation.ga_num_generations [27000]This is the maximum number of generations simulated during each GA or LGA calculation.ga_elitism [1]This is used in the selection mechanism of the GA. This is the number of top individuals that areguaranteed to survive into the next generation.ga_mutation_rate [0.02]This is a floating point number from 0 to 1, representing the probability that a particular gene ismutated. This parameter is typically small.ga_crossover_rate [0.80]This is a floating point number from 0 to 1 denoting the crossover rate. Crossover rate is theexpected number of pairs in the population that will exchange genetic material. Setting this value to0 turns the GA into the evolutionary programming (EP) method, but EP would probably require aconcomitant increase in the ga_mutation_rate in order to be effective.ga_window_size40
[10]This is the number of preceding generations to take into consideration when deciding the thresholdfor the worst individual in the current population.ga_cauchy_alpha[0.0]ga_cauchy_beta [1.0]These are floating point parameters used in the mutation of real number genes. They correspond tothe alpha and beta parameters in a Cauchy distribution. Alpha roughly corresponds to the mean,and beta to something like the variance of the distribution. It should be noted, though, that theCauchy distribution doesn’t have finite variance. For the mutation of a real valued gene, a Cauchydeviate is generated and then added to the original value.Genetic algorithm parametersset_gaThis command sets the global optimizer to be a genetic algorithm [GA]. This is required to performa GA search. This passes any ’ga_’ parameters specified before this line to the global optimizerobject. If this command is omitted, or it is given before the ’ga_’ parameters, your choices will nottake effect, and the default values for the optimizer will be used.To use the traditional (non-Lamarckian) genetic algorithm, do not specify the local searchparameters, and do not use the “set_sw1” or “set_psw1” commands.To use the Lamarckian genetic algorithm, you must also specify the parameters for local search,and then issue either the ’set_sw1’ or ’set_psw1’ command. The ’set_sw1’ command uses thestrict Solis and Wets local search algorithm, while ’set_psw1’uses the pseudo-Solis and Wetsalgorithm (see below).Parameters for local searchsw_max_its [300]This is the maximum number of iterations that the local search procedure apply to the phenotype ofany given individual.sw_max_succ [4]This is the number of successes in a row before a change is made to the “rho” parameter in Solis& Wets algorithms. This is an unsigned integer and is typically around four.sw_max_fail [4]This is the number of failures in a row before Solis & Wets algorithms adjust “rho.” This is anunsigned integer and is usually around four.41
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 and 20: “unbound_model_extended.” This
Page 21 and 22: STEP 4: Evaluating the Results of a
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: is small enough to fit into the low
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

AutoDock Version 4.2

Create successful ePaper yourself

Delete template?

Save as template?