Flex.in
From Rizzo_Lab
ligand_atom_file ./ligand_charged.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol no orient_ligand yes automated_matching yes receptor_site_file ./selected_spheres.sph max_orientations 500 critical_points no chemical_matching no use_ligand_spheres no flexible_ligand yes min_anchor_size 40 pruning_use_clustering yes pruning_max_orients 100 pruning_clustering_cutoff 100 use_internal_energy yes internal_energy_att_exp 6 internal_energy_rep_exp 12 internal_energy_dielectric 4.0 use_clash_overlap 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 grid dock3.5_score_secondary no continuous_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_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_final_min no simplex_random_seed 0 atom_model all vdw_defn_file /home/rizzo/AMS536software/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /home/rizzo/AMS536software/dock6/parameters/flex.defn flex_drive_file /home/rizzo/AMS536software/dock6/parameters/flex_drive.tbl ligand_outfile_prefix flex write_orientations no num_scored_conformers 50 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
