Difference between revisions of "Joe and Brian de novo stuff"
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dn_user_specified_anchor no | dn_user_specified_anchor no | ||
dn_use_torenv_table yes | dn_use_torenv_table yes | ||
| − | dn_torenv_table ../002.generate-frags/fraglib_torenv.dat | + | dn_torenv_table ../002.generate-frags/fraglib_torenv.dat |
| − | dn_sampling_method ex | + | dn_sampling_method ex |
| − | dn_pruning_conformer_score_cutoff 200.0 | + | dn_pruning_conformer_score_cutoff 200.0 |
| − | dn_torsion_rmsd_cutoff 0.5 | + | dn_torsion_rmsd_cutoff 0.5 |
| − | dn_constraint_mol_wt 800 | + | dn_constraint_mol_wt 800 |
| − | dn_constraint_rot_bon 12 | + | dn_constraint_rot_bon 12 |
| − | dn_constraint_formal_charge 2.0 | + | dn_constraint_formal_charge 2.0 |
| − | dn_constraint_charge_groups 6 | + | dn_constraint_charge_groups 6 |
| − | dn_tanimoto_cutoff 0.8 | + | dn_tanimoto_cutoff 0.8 |
| − | dn_heur_unmatched_num 2 | + | dn_heur_unmatched_num 2 |
| − | dn_heur_matched_rmsd 2.0 | + | dn_heur_matched_rmsd 2.0 |
| − | dn_max_grow_layers 7 | + | dn_max_grow_layers 7 |
| − | dn_max_current_aps 7 | + | dn_max_current_aps 7 |
| − | dn_max_root_size 40 | + | dn_max_root_size 40 |
| − | dn_max_layer_size 40 | + | dn_max_layer_size 40 |
| − | dn_write_checkpoints no | + | dn_write_checkpoints no |
| − | dn_write_orients no | + | dn_write_orients no |
| − | dn_write_growth_trees no | + | dn_write_growth_trees no |
| − | dn_output_prefix final | + | dn_output_prefix final |
| − | use_internal_energy yes | + | use_internal_energy yes |
| − | internal_energy_rep_exp 12 | + | internal_energy_rep_exp 12 |
| − | use_database_filter no | + | use_database_filter no |
| − | orient_ligand yes | + | orient_ligand yes |
| − | automated_matching yes | + | automated_matching yes |
| − | receptor_site_file ../001.files/1FPU.rec.clust.close.sph | + | receptor_site_file ../001.files/1FPU.rec.clust.close.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 |
| − | ph4_score_primary no | + | ph4_score_primary no |
| − | ph4_score_secondary no | + | ph4_score_secondary no |
| − | descriptor_score_primary yes | + | descriptor_score_primary yes |
| − | descriptor_score_secondary no | + | descriptor_score_secondary no |
| − | descriptor_use_grid_score yes | + | descriptor_use_grid_score yes |
| − | descriptor_use_pharmacophore_score no | + | descriptor_use_pharmacophore_score no |
| − | descriptor_use_tanimoto yes | + | descriptor_use_tanimoto yes |
| − | descriptor_use_hungarian yes | + | descriptor_use_hungarian yes |
| − | descriptor_grid_score_rep_rad_scale 1 | + | descriptor_grid_score_rep_rad_scale 1 |
| − | descriptor_grid_score_vdw_scale 1 | + | descriptor_grid_score_vdw_scale 1 |
| − | descriptor_grid_score_es_scale 1 | + | descriptor_grid_score_es_scale 1 |
| − | descriptor_grid_score_grid_prefix ../001.files/1FPU.rec | + | descriptor_grid_score_grid_prefix ../001.files/1FPU.rec |
| − | descriptor_fingerprint_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 | + | descriptor_fingerprint_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 |
| − | descriptor_hungarian_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 | + | descriptor_hungarian_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 |
| − | descriptor_hungarian_matching_coeff -5 | + | descriptor_hungarian_matching_coeff -5 |
| − | descriptor_hungarian_rmsd_coeff 1 | + | descriptor_hungarian_rmsd_coeff 1 |
| − | descriptor_weight_grid_score 1 | + | descriptor_weight_grid_score 1 |
| − | descriptor_weight_fingerprint_tanimoto 0 | + | descriptor_weight_fingerprint_tanimoto 0 |
| − | descriptor_weight_hungarian 0 | + | descriptor_weight_hungarian 0 |
| − | gbsa_zou_score_secondary no | + | gbsa_zou_score_secondary no |
| − | gbsa_hawkins_score_secondary no | + | gbsa_hawkins_score_secondary no |
| − | SASA_descriptor_score_secondary no | + | SASA_descriptor_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 20 | + | simplex_grow_max_iterations 20 |
| − | 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 | + | simplex_coefficient_restraint 10 |
| − | atom_model all | + | atom_model all |
| − | vdw_defn_file ../zzz.dock-files/vdw_AMBER_parm99.defn | + | vdw_defn_file ../zzz.dock-files/vdw_AMBER_parm99.defn |
| − | flex_defn_file ../zzz.dock-files/flex.defn | + | flex_defn_file ../zzz.dock-files/flex.defn |
| − | flex_drive_file ../zzz.dock-files/flex_drive.tbl | + | flex_drive_file ../zzz.dock-files/flex_drive.tbl |
Revision as of 11:31, 15 September 2015
This is our secret wiki page.
This is the version of the code on cluster that we should be using
/sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper
/sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper/src/dock/dock6
This is the input file we should be using
conformer_search_type denovo dn_fraglib_scaffold_file ../002.generate-frags/fraglib_scaffold.mol2 dn_fraglib_linker_file ../002.generate-frags/fraglib_linker.mol2 dn_fraglib_sidechain_file ../002.generate-frags/fraglib_sidechain.mol2 dn_user_specified_anchor no dn_use_torenv_table yes dn_torenv_table ../002.generate-frags/fraglib_torenv.dat dn_sampling_method ex dn_pruning_conformer_score_cutoff 200.0 dn_torsion_rmsd_cutoff 0.5 dn_constraint_mol_wt 800 dn_constraint_rot_bon 12 dn_constraint_formal_charge 2.0 dn_constraint_charge_groups 6 dn_tanimoto_cutoff 0.8 dn_heur_unmatched_num 2 dn_heur_matched_rmsd 2.0 dn_max_grow_layers 7 dn_max_current_aps 7 dn_max_root_size 40 dn_max_layer_size 40 dn_write_checkpoints no dn_write_orients no dn_write_growth_trees no dn_output_prefix final use_internal_energy yes internal_energy_rep_exp 12 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../001.files/1FPU.rec.clust.close.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 ph4_score_primary no ph4_score_secondary no descriptor_score_primary yes descriptor_score_secondary no descriptor_use_grid_score yes descriptor_use_pharmacophore_score no descriptor_use_tanimoto yes descriptor_use_hungarian yes descriptor_grid_score_rep_rad_scale 1 descriptor_grid_score_vdw_scale 1 descriptor_grid_score_es_scale 1 descriptor_grid_score_grid_prefix ../001.files/1FPU.rec descriptor_fingerprint_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 descriptor_hungarian_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 descriptor_hungarian_matching_coeff -5 descriptor_hungarian_rmsd_coeff 1 descriptor_weight_grid_score 1 descriptor_weight_fingerprint_tanimoto 0 descriptor_weight_hungarian 0 gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_descriptor_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 20 simplex_grow_tors_premin_iterations 0 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10 atom_model all vdw_defn_file ../zzz.dock-files/vdw_AMBER_parm99.defn flex_defn_file ../zzz.dock-files/flex.defn flex_drive_file ../zzz.dock-files/flex_drive.tbl
