Difference between revisions of "DOCK CV Input File(s)"
From Rizzo_Lab
(Created page with "This is a standard input file for de novo DOCK6 using multigrid score through descriptor score. conformer_search_type covalent prunin...") |
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| − | This is a standard input file for | + | This is a standard input file for covalent DOCK6 using grid score. The essential parameters for DOCKovalent are highlighted in '''bold'''. |
| − | conformer_search_type covalent | + | '''conformer_search_type covalent''' |
| − | pruning_use_clustering yes | + | '''pruning_use_clustering yes''' |
| − | pruning_max_orients 100 | + | '''pruning_max_orients 100''' |
| − | pruning_clustering_cutoff 100 | + | '''pruning_clustering_cutoff 100''' |
| − | pruning_conformer_score_cutoff 100.0 | + | '''pruning_conformer_score_cutoff 100.0''' |
use_clash_overlap no | use_clash_overlap no | ||
| − | write_growth_tree | + | write_growth_tree no |
use_internal_energy yes | use_internal_energy yes | ||
internal_energy_rep_exp 12 | internal_energy_rep_exp 12 | ||
| Line 17: | Line 17: | ||
calculate_rmsd no | calculate_rmsd no | ||
use_database_filter no | use_database_filter no | ||
| − | orient_ligand yes | + | '''orient_ligand yes''' |
automated_matching yes | automated_matching yes | ||
receptor_site_file rec_sph.sph | receptor_site_file rec_sph.sph | ||
| Line 46: | Line 46: | ||
SASA_score_secondary no | SASA_score_secondary no | ||
amber_score_secondary no | amber_score_secondary no | ||
| − | minimize_ligand yes | + | '''minimize_ligand yes''' |
| − | minimize_anchor no | + | '''minimize_anchor no''' |
| − | 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 | ||
| Line 56: | Line 56: | ||
simplex_rot_step 0.1 | simplex_rot_step 0.1 | ||
simplex_tors_step 10.0 | simplex_tors_step 10.0 | ||
| − | simplex_grow_max_iterations 0 | + | '''simplex_grow_max_iterations 0''' |
| − | simplex_grow_tors_premin_iterations 1000 | + | '''simplex_grow_tors_premin_iterations 1000''' |
simplex_random_seed 0 | simplex_random_seed 0 | ||
simplex_restraint_min yes | simplex_restraint_min yes | ||
Latest revision as of 16:16, 14 May 2019
This is a standard input file for covalent DOCK6 using grid score. The essential parameters for DOCKovalent are highlighted in bold.
conformer_search_type covalent pruning_use_clustering yes pruning_max_orients 100 pruning_clustering_cutoff 100 pruning_conformer_score_cutoff 100.0 use_clash_overlap no write_growth_tree no use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file ligand.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand yes automated_matching yes receptor_site_file rec_sph.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 yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix rec.grid gist_score_secondary no multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no pharmacophore_score_secondary no hbond_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand yes minimize_anchor no 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_grow_max_iterations 0 simplex_grow_tors_premin_iterations 1000 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10.0 atom_model all vdw_defn_file vdw_AMBER_parm99.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl ligand_outfile_prefix output_rs write_orientations no num_scored_conformers 1000 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
