Difference between revisions of "Example of an Input file"
From Rizzo_Lab
Stonybrook (talk | contribs) (Created page with "This is a standard input file for de novo DOCK6 using multigrid score through descriptor score. conformer_search_type denovo dn_fraglib...") |
|||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
This is a standard input file for de novo DOCK6 using multigrid score through descriptor score. | This is a standard input file for de novo DOCK6 using multigrid score through descriptor score. | ||
| − | conformer_search_type denovo | + | conformer_search_type denovo |
| − | dn_fraglib_scaffold_file / | + | dn_fraglib_scaffold_file /PATH/gen-frags-12/fraglib_scaffold.mol2 |
| − | dn_fraglib_linker_file / | + | dn_fraglib_linker_file /PATH/gen-frags-12/fraglib_linker.mol2 |
| − | dn_fraglib_sidechain_file / | + | dn_fraglib_sidechain_file /PATH/gen-frags-12/fraglib_sidechain.mol2 |
| − | dn_user_specified_anchor yes | + | dn_user_specified_anchor yes |
| − | dn_fraglib_anchor_file / | + | dn_fraglib_anchor_file /PATH/01.files/anchor.mol2 |
| − | dn_use_torenv_table yes | + | dn_use_torenv_table yes |
| − | dn_torenv_table / | + | dn_torenv_table /PATH/gen-frags-12/fraglib_torenv.dat |
| − | dn_sampling_method graph | + | dn_sampling_method graph |
| − | dn_graph_max_picks 30 | + | dn_graph_max_picks 30 |
| − | dn_graph_breadth 3 | + | dn_graph_breadth 3 |
| − | dn_graph_depth 2 | + | dn_graph_depth 2 |
| − | dn_graph_temperature 100 | + | dn_graph_temperature 100 |
| − | dn_pruning_conformer_score_cutoff 100.0 | + | dn_pruning_conformer_score_cutoff 100.0 |
| − | dn_pruning_conformer_score_scaling_factor 2.0 | + | dn_pruning_conformer_score_scaling_factor 2.0 |
| − | dn_pruning_clustering_cutoff 100.0 | + | dn_pruning_clustering_cutoff 100.0 |
| − | dn_constraint_mol_wt | + | dn_constraint_mol_wt 550 |
| − | dn_constraint_rot_bon 15 | + | dn_constraint_rot_bon 15 |
| − | dn_constraint_formal_charge 2.0 | + | dn_constraint_formal_charge 2.0 |
| − | dn_heur_unmatched_num 1 | + | dn_heur_unmatched_num 1 |
| − | dn_heur_matched_rmsd 2.0 | + | dn_heur_matched_rmsd 2.0 |
| − | dn_unique_anchors 1 | + | dn_unique_anchors 1 |
| − | dn_max_grow_layers 2 | + | dn_max_grow_layers 2 |
| − | dn_max_root_size 25 | + | dn_max_root_size 25 |
| − | dn_max_layer_size 25 | + | dn_max_layer_size 25 |
| − | dn_max_current_aps 5 | + | dn_max_current_aps 5 |
| − | dn_max_scaffolds_per_layer 1 | + | dn_max_scaffolds_per_layer 1 |
| − | dn_write_checkpoints yes | + | dn_write_checkpoints yes |
| − | dn_write_prune_dump yes | + | dn_write_prune_dump yes |
| − | dn_write_orients no | + | dn_write_orients no |
| − | dn_write_growth_trees no | + | dn_write_growth_trees no |
| − | dn_output_prefix | + | dn_output_prefix final |
| − | 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 yes | + | orient_ligand yes |
| − | automated_matching yes | + | automated_matching yes |
| − | receptor_site_file / | + | receptor_site_file /PATH/01.files/spheres.sph |
| − | max_orientations 1000 | + | max_orientations 1000 |
| − | critical_points no | + | critical_points no |
| − | chemical_matching no | + | chemical_matching no |
| − | use_ligand_spheres no | + | use_ligand_spheres 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 | + | descriptor_multigrid_score_rep_rad_scale 1 |
| − | descriptor_multigrid_score_vdw_scale 1 | + | descriptor_multigrid_score_vdw_scale 1 |
| − | descriptor_multigrid_score_es_scale 1 | + | descriptor_multigrid_score_es_scale 1 |
| − | descriptor_multigrid_score_number_of_grids 14 | + | descriptor_multigrid_score_number_of_grids 14 |
| − | descriptor_multigrid_score_grid_prefix0 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix0 ../../07.multigrid/SYSTEM.resid_025 |
| − | descriptor_multigrid_score_grid_prefix1 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix1 ../../07.multigrid/SYSTEM.resid_028 |
| − | descriptor_multigrid_score_grid_prefix2 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix2 ../../07.multigrid/SYSTEM.resid_029 |
| − | descriptor_multigrid_score_grid_prefix3 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix3 ../../07.multigrid/SYSTEM.resid_032 |
| − | descriptor_multigrid_score_grid_prefix4 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix4 ../../07.multigrid/SYSTEM.resid_036 |
| − | descriptor_multigrid_score_grid_prefix5 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix5 ../../07.multigrid/SYSTEM.resid_092 |
| − | descriptor_multigrid_score_grid_prefix6 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix6 ../../07.multigrid/SYSTEM.resid_095 |
| − | descriptor_multigrid_score_grid_prefix7 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix7 ../../07.multigrid/SYSTEM.resid_096 |
| − | descriptor_multigrid_score_grid_prefix8 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix8 ../../07.multigrid/SYSTEM.resid_098 |
| − | descriptor_multigrid_score_grid_prefix9 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix9 ../../07.multigrid/SYSTEM.resid_099 |
| − | descriptor_multigrid_score_grid_prefix10 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix10 ../../07.multigrid/SYSTEM.resid_102 |
| − | descriptor_multigrid_score_grid_prefix11 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix11 ../../07.multigrid/SYSTEM.resid_103 |
| − | descriptor_multigrid_score_grid_prefix12 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix12 ../../07.multigrid/SYSTEM.resid_106 |
| − | descriptor_multigrid_score_grid_prefix13 ../../07.multigrid/ | + | descriptor_multigrid_score_grid_prefix13 ../../07.multigrid/SYSTEM.resid_remaining |
| − | descriptor_multigrid_score_fp_ref_mol yes | + | descriptor_multigrid_score_fp_ref_mol yes |
| − | descriptor_multigrid_score_footprint_ref / | + | descriptor_multigrid_score_footprint_ref /PATH/01.files/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 no | + | simplex_restraint_min no |
| − | atom_model all | + | atom_model all |
| − | vdw_defn_file / | + | vdw_defn_file /PATH/dock6/parameters/vdw_AMBER_parm99.defn |
| − | flex_defn_file / | + | flex_defn_file /PATH/dock6/parameters/flex.defn |
| − | flex_drive_file / | + | flex_drive_file /PATH/dock6/parameters/flex_drive.tbl |
Latest revision as of 13:46, 6 September 2018
This is a standard input file for de novo DOCK6 using multigrid score through descriptor score.
conformer_search_type denovo dn_fraglib_scaffold_file /PATH/gen-frags-12/fraglib_scaffold.mol2 dn_fraglib_linker_file /PATH/gen-frags-12/fraglib_linker.mol2 dn_fraglib_sidechain_file /PATH/gen-frags-12/fraglib_sidechain.mol2 dn_user_specified_anchor yes dn_fraglib_anchor_file /PATH/01.files/anchor.mol2 dn_use_torenv_table yes dn_torenv_table /PATH/gen-frags-12/fraglib_torenv.dat dn_sampling_method graph dn_graph_max_picks 30 dn_graph_breadth 3 dn_graph_depth 2 dn_graph_temperature 100 dn_pruning_conformer_score_cutoff 100.0 dn_pruning_conformer_score_scaling_factor 2.0 dn_pruning_clustering_cutoff 100.0 dn_constraint_mol_wt 550 dn_constraint_rot_bon 15 dn_constraint_formal_charge 2.0 dn_heur_unmatched_num 1 dn_heur_matched_rmsd 2.0 dn_unique_anchors 1 dn_max_grow_layers 2 dn_max_root_size 25 dn_max_layer_size 25 dn_max_current_aps 5 dn_max_scaffolds_per_layer 1 dn_write_checkpoints yes dn_write_prune_dump yes dn_write_orients no dn_write_growth_trees no dn_output_prefix final use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file /PATH/01.files/spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres 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 descriptor_multigrid_score_vdw_scale 1 descriptor_multigrid_score_es_scale 1 descriptor_multigrid_score_number_of_grids 14 descriptor_multigrid_score_grid_prefix0 ../../07.multigrid/SYSTEM.resid_025 descriptor_multigrid_score_grid_prefix1 ../../07.multigrid/SYSTEM.resid_028 descriptor_multigrid_score_grid_prefix2 ../../07.multigrid/SYSTEM.resid_029 descriptor_multigrid_score_grid_prefix3 ../../07.multigrid/SYSTEM.resid_032 descriptor_multigrid_score_grid_prefix4 ../../07.multigrid/SYSTEM.resid_036 descriptor_multigrid_score_grid_prefix5 ../../07.multigrid/SYSTEM.resid_092 descriptor_multigrid_score_grid_prefix6 ../../07.multigrid/SYSTEM.resid_095 descriptor_multigrid_score_grid_prefix7 ../../07.multigrid/SYSTEM.resid_096 descriptor_multigrid_score_grid_prefix8 ../../07.multigrid/SYSTEM.resid_098 descriptor_multigrid_score_grid_prefix9 ../../07.multigrid/SYSTEM.resid_099 descriptor_multigrid_score_grid_prefix10 ../../07.multigrid/SYSTEM.resid_102 descriptor_multigrid_score_grid_prefix11 ../../07.multigrid/SYSTEM.resid_103 descriptor_multigrid_score_grid_prefix12 ../../07.multigrid/SYSTEM.resid_106 descriptor_multigrid_score_grid_prefix13 ../../07.multigrid/SYSTEM.resid_remaining descriptor_multigrid_score_fp_ref_mol yes descriptor_multigrid_score_footprint_ref /PATH/01.files/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 no 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
