Example of an Ensemble Evolution Input file

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This is a standard input file for GA in DOCK6 using multigrid score through descriptor score. Anything dictated with a "PATH" must be changed to work for each user.

conformer_search_type                                        genetic
ga_molecule_file                                             /PATH/zzz.GA_parent_molecules.mol2
ga_fraglib_scaffold_file                                     /PATH/fraglib_scaffold.mol2
ga_fraglib_linker_file                                       /PATH/fraglib_linker.mol2
ga_fraglib_sidechain_file                                    /PATH/fraglib_sidechain.mol2
ga_torenv_table                                              /PATH/torenv_table.dat
ga_max_generations                                           500
ga_xover_sampling_method_rand                                yes
ga_xover_max                                                 150
ga_bond_tolerance                                            0.5
ga_angle_cutoff                                              0.14
ga_check_overlap                                             no
ga_mutate_parents                                            no
ga_pmut_rate                                                 0.3
ga_omut_rate                                                 0.7
ga_max_mut_cycles                                            5
ga_mut_sampling_method                                       rand
ga_num_random_picks                                          10
ga_max_root_size                                             5
ga_energy_cutoff                                             100
ga_heur_unmatched_num                                        1
ga_heur_matched_rmsd                                         2.0
ga_constraint_mol_wt                                         550
ga_constraint_rot_bon                                        10
ga_constraint_H_accept                                       10
ga_constraint_H_don                                          5
ga_constraint_formal_charge                                  4
ga_ensemble_size                                             200
ga_selection_method                                          elitism
ga_elitism_combined                                          no
ga_elitism_option                                            max
ga_niching                                                   no
ga_selection_extinction                                      no
ga_max_num_gen_with_no_crossover                             50
ga_output_prefix                                             OUTPUT
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
footprint_similarity_score_primary                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    no
descriptor_use_multigrid_score                               yes
descriptor_use_pharmacophore_score                           no
descriptor_use_tanimoto                                      no
descriptor_use_hungarian                                     no
descriptor_use_volume_overlap                                no
descriptor_multigrid_score_rep_rad_scale                     1.0
descriptor_multigrid_score_vdw_scale                         1.0
descriptor_multigrid_score_es_scale                          1.0
descriptor_multigrid_score_number_of_grids                   3
descriptor_multigrid_score_grid_prefix0                      /PATH/1A52.resid_039
descriptor_multigrid_score_grid_prefix1                      /PATH/1A52.resid_042
descriptor_multigrid_score_grid_prefix16                     /PATH/1A52.resid_remaining
descriptor_multigrid_score_fp_ref_mol                        yes
descriptor_multigrid_score_footprint_ref                     /PATH/1A52.1A52.lig.multigridmin.mol2
descriptor_multigrid_score_foot_compare_type                 Euclidean
descriptor_multigrid_score_normalize_foot                    no
descriptor_multigrid_score_vdw_euc_scale                     1.0
descriptor_multigrid_score_es_euc_scale                      1.0
descriptor_weight_multigrid_score                            1
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_anchor_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_grow_tors_premin_iterations                          0
simplex_random_seed                                          0
simplex_restraint_min                                        yes
simplex_coefficient_restraint                                10.0
atom_model                                                   all
vdw_defn_file                                                /PATH/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /PATH/dock6/parameters/flex.defn
flex_drive_file                                              /PATH/dock6/parameters/flex_drive.tbl