ligand_atom_file                                             ./rpr.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       yes
rmsd_reference_filename                                      ./rpr_xray.mol2
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ./selected_spheres.sph
max_orientations                                             100
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              yes
min_anchor_size                                              50
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                                         yes
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ./grid
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                                  10
simplex_final_min                                            no
simplex_secondary_minimize_pose                              no
simplex_random_seed                                          0
atom_model                                                   all
vdw_defn_file                                                /usr/local/dock/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /usr/local/dock/parameters/flex.defn
flex_drive_file                                              /usr/local/dock/parameters/flex_drive.tbl
ligand_outfile_prefix                                        rpr
write_orientations                                           yes
num_primary_scored_conformers_rescored                       10
cluster_primary_conformations                                yes
cluster_rmsd_threshold                                       2.0
num_clusterheads_for_rescore                                 5
num_secondary_scored_conformers_written                      1
rank_primary_ligands                                         no
rank_secondary_ligands                                       no