Difference between revisions of "Example of an CONGA Input file"
From Rizzo_Lab
(Created page with "This is a standard input file for CONGA in DOCK6 using multigrid score through descriptor score. Anything dictated with a "PATH" must be changed to work for each user. confor...") |
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Anything dictated with a "PATH" must be changed to work for each user. | Anything dictated with a "PATH" must be changed to work for each user. | ||
| − | conformer_search_type conga | + | conformer_search_type conga |
| − | ga_molecule_file /PATH/zzz.GA_parent_molecules.mol2 | + | ga_molecule_file /PATH/zzz.GA_parent_molecules.mol2 |
| − | ga_fraglib_scaffold_file /PATH/fraglib_scaffold.mol2 | + | ga_fraglib_scaffold_file /PATH/fraglib_scaffold.mol2 |
| − | ga_fraglib_linker_file /PATH/fraglib_linker.mol2 | + | ga_fraglib_linker_file /PATH/fraglib_linker.mol2 |
| − | ga_fraglib_sidechain_file /PATH/fraglib_sidechain.mol2 | + | ga_fraglib_sidechain_file /PATH/fraglib_sidechain.mol2 |
| − | ga_torenv_table /PATH/torenv_table.dat | + | ga_torenv_table /PATH/torenv_table.dat |
| − | ga_max_generations 1000 | + | ga_max_generations 1000 |
| − | ga_xover_sampling_method_rand yes | + | ga_xover_sampling_method_rand yes |
| − | ga_xover_max 150 | + | ga_xover_max 150 |
| − | ga_bond_tolerance 0.5 | + | ga_bond_tolerance 0.5 |
| − | ga_angle_cutoff 0.14 | + | ga_angle_cutoff 0.14 |
| − | ga_check_overlap no | + | ga_check_overlap no |
| − | ga_mutate_parents yes | + | ga_mutate_parents yes |
| − | ga_pmut_rate 0.3 | + | ga_pmut_rate 0.3 |
| − | ga_omut_rate 0.7 | + | ga_omut_rate 0.7 |
| − | ga_max_mut_cycles 5 | + | ga_max_mut_cycles 5 |
| − | ga_mut_sampling_method rand | + | ga_mut_sampling_method rand |
| − | ga_num_random_picks 10 | + | ga_num_random_picks 10 |
| − | ga_max_root_size 5 | + | ga_max_root_size 5 |
| − | ga_energy_cutoff 100 | + | ga_energy_cutoff 100 |
| − | ga_heur_unmatched_num 1 | + | ga_heur_unmatched_num 1 |
| − | ga_heur_matched_rmsd 2.0 | + | ga_heur_matched_rmsd 2.0 |
| − | ga_constraint_mol_wt ] | + | ga_constraint_mol_wt ] |
| − | ga_constraint_rot_bon 10 | + | ga_constraint_rot_bon 10 |
| − | ga_constraint_H_accept 10 | + | ga_constraint_H_accept 10 |
| − | ga_constraint_H_don 5 | + | ga_constraint_H_don 5 |
| − | ga_constraint_formal_charge 4 | + | ga_constraint_formal_charge 4 |
| − | ga_ensemble_size 200 | + | ga_ensemble_size 200 |
| − | ga_selection_method elitism | + | ga_selection_method elitism |
| − | ga_elitism_combined no | + | ga_elitism_combined no |
| − | ga_elitism_option max | + | ga_elitism_option max |
| − | ga_niching no | + | ga_niching no |
| − | ga_selection_extinction no | + | ga_selection_extinction no |
| − | ga_max_num_gen_with_no_crossover 1000 | + | ga_max_num_gen_with_no_crossover 1000 |
| − | ga_output_prefix OUTPUT | + | ga_output_prefix OUTPUT |
| − | use_internal_energy yes | + | use_internal_energy yes |
| − | internal_energy_rep_exp 12 | + | internal_energy_rep_exp 12 |
| − | internal_energy_cutoff 100.0 | + | internal_energy_cutoff 100.0 |
| − | use_database_filter no | + | use_database_filter no |
| − | orient_ligand no | + | orient_ligand no |
| − | bump_filter no | + | bump_filter no |
| − | score_molecules yes | + | score_molecules yes |
| − | contact_score_primary no | + | contact_score_primary no |
| − | contact_score_secondary no | + | contact_score_secondary no |
| − | grid_score_primary no | + | grid_score_primary no |
| − | grid_score_secondary no | + | grid_score_secondary no |
| − | multigrid_score_primary no | + | multigrid_score_primary no |
| − | multigrid_score_secondary no | + | multigrid_score_secondary no |
| − | dock3.5_score_primary no | + | dock3.5_score_primary no |
| − | dock3.5_score_secondary no | + | dock3.5_score_secondary no |
| − | continuous_score_primary no | + | continuous_score_primary no |
| − | continuous_score_secondary no | + | continuous_score_secondary no |
| − | footprint_similarity_score_primary no | + | footprint_similarity_score_primary no |
| − | footprint_similarity_score_secondary no | + | footprint_similarity_score_secondary no |
| − | pharmacophore_score_primary no | + | pharmacophore_score_primary no |
| − | pharmacophore_score_secondary no | + | pharmacophore_score_secondary no |
| − | descriptor_score_primary yes | + | descriptor_score_primary yes |
| − | descriptor_score_secondary no | + | descriptor_score_secondary no |
| − | descriptor_use_grid_score no | + | descriptor_use_grid_score no |
| − | descriptor_use_multigrid_score yes | + | descriptor_use_multigrid_score yes |
| − | descriptor_use_pharmacophore_score no | + | descriptor_use_pharmacophore_score no |
| − | descriptor_use_tanimoto no | + | descriptor_use_tanimoto no |
| − | descriptor_use_hungarian no | + | descriptor_use_hungarian no |
| − | descriptor_use_volume_overlap no | + | descriptor_use_volume_overlap no |
| − | descriptor_multigrid_score_rep_rad_scale 1.0 | + | descriptor_multigrid_score_rep_rad_scale 1.0 |
| − | descriptor_multigrid_score_vdw_scale 1.0 | + | descriptor_multigrid_score_vdw_scale 1.0 |
| − | descriptor_multigrid_score_es_scale 1.0 | + | descriptor_multigrid_score_es_scale 1.0 |
| − | descriptor_multigrid_score_number_of_grids 3 | + | descriptor_multigrid_score_number_of_grids 3 |
| − | descriptor_multigrid_score_grid_prefix0 /PATH/1A52.resid_039 | + | descriptor_multigrid_score_grid_prefix0 /PATH/1A52.resid_039 |
| − | descriptor_multigrid_score_grid_prefix1 /PATH/1A52.resid_042 | + | descriptor_multigrid_score_grid_prefix1 /PATH/1A52.resid_042 |
| − | descriptor_multigrid_score_grid_prefix16 /PATH/1A52.resid_remaining | + | descriptor_multigrid_score_grid_prefix16 /PATH/1A52.resid_remaining |
| − | descriptor_multigrid_score_fp_ref_mol yes | + | descriptor_multigrid_score_fp_ref_mol yes |
| − | descriptor_multigrid_score_footprint_ref /PATH/1A52.1A52.lig.multigridmin.mol2 | + | descriptor_multigrid_score_footprint_ref /PATH/1A52.1A52.lig.multigridmin.mol2 |
| − | descriptor_multigrid_score_foot_compare_type Euclidean | + | descriptor_multigrid_score_foot_compare_type Euclidean |
| − | descriptor_multigrid_score_normalize_foot no | + | descriptor_multigrid_score_normalize_foot no |
| − | descriptor_multigrid_score_vdw_euc_scale 1.0 | + | descriptor_multigrid_score_vdw_euc_scale 1.0 |
| − | descriptor_multigrid_score_es_euc_scale 1.0 | + | descriptor_multigrid_score_es_euc_scale 1.0 |
| − | descriptor_weight_multigrid_score 1 | + | descriptor_weight_multigrid_score 1 |
| − | gbsa_zou_score_secondary no | + | gbsa_zou_score_secondary no |
| − | gbsa_hawkins_score_secondary no | + | gbsa_hawkins_score_secondary no |
| − | SASA_score_secondary no | + | SASA_score_secondary no |
| − | amber_score_secondary no | + | amber_score_secondary no |
| − | minimize_ligand yes | + | minimize_ligand yes |
| − | minimize_anchor yes | + | minimize_anchor yes |
| − | minimize_flexible_growth yes | + | minimize_flexible_growth yes |
| − | use_advanced_simplex_parameters no | + | use_advanced_simplex_parameters no |
| − | simplex_max_cycles 1 | + | simplex_max_cycles 1 |
| − | simplex_score_converge 0.1 | + | simplex_score_converge 0.1 |
| − | simplex_cycle_converge 1.0 | + | simplex_cycle_converge 1.0 |
| − | simplex_trans_step 1.0 | + | simplex_trans_step 1.0 |
| − | simplex_rot_step 0.1 | + | simplex_rot_step 0.1 |
| − | simplex_tors_step 10.0 | + | simplex_tors_step 10.0 |
| − | simplex_anchor_max_iterations 500 | + | simplex_anchor_max_iterations 500 |
| − | simplex_grow_max_iterations 500 | + | simplex_grow_max_iterations 500 |
| − | simplex_grow_tors_premin_iterations 0 | + | simplex_grow_tors_premin_iterations 0 |
| − | simplex_random_seed 0 | + | simplex_random_seed 0 |
| − | simplex_restraint_min yes | + | simplex_restraint_min yes |
| − | simplex_coefficient_restraint 10.0 | + | simplex_coefficient_restraint 10.0 |
| − | atom_model all | + | atom_model all |
| − | vdw_defn_file /PATH/dock6/parameters/vdw_AMBER_parm99.defn | + | vdw_defn_file /PATH/dock6/parameters/vdw_AMBER_parm99.defn |
| − | flex_defn_file /PATH/dock6/parameters/flex.defn | + | flex_defn_file /PATH/dock6/parameters/flex.defn |
| − | flex_drive_file /PATH/dock6/parameters/flex_drive.tbl | + | flex_drive_file /PATH/dock6/parameters/flex_drive.tbl |
Revision as of 13:40, 28 August 2018
This is a standard input file for CONGA in DOCK6 using multigrid score through descriptor score. Anything dictated with a "PATH" must be changed to work for each user.
conformer_search_type conga 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 ] 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
