Example of an Single Molecule Evolution Input file
From Rizzo_Lab
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 1000 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 yes 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 1000 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
