DOCK CV Input File(s)
From Rizzo_Lab
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
