[DISPLAY PARAMETERIZED DOCK INPUT File]

bezek:~/ng/mm/dock_inputs> cat dock_base
flexible_ligand                $flexible_ligand
orient_ligand                  $orient_ligand
score_ligand                   $score_ligand
minimize_ligand                $minimize_ligand
multiple_ligands               $multiple_ligands
random_seed                    $random_seed
anchor_search                  $anchor_search
torsion_drive                  $torsion_drive
clash_overlap                  $clash_overlap
conformation_cutoff_factor     $conformation_cutoff_factor
torsion_minimize               $torsion_minimize
match_receptor_sites           $match_receptor_sites
random_search                  $random_search
ligand_centers                 $ligand_centers
maximum_orientations           $maximum_orientations
write_configurations           $write_configurations
rank_orientations              $rank_orientations
rank_orientation_total         $rank_orientation_total
write_configuration_total      $write_configuration_total
intramolecular_score           $intramolecular_score
intermolecular_score           $intermolecular_score
gridded_score                  $gridded_score
grid_version                   $grid_version
bump_filter                    $bump_filter
bump_maximum                   $bump_maximum
contact_score                  $contact_score
contact_cutoff_distance        $contact_cutoff_distance
contact_clash_overlap          $contact_clash_overlap
contact_clash_penalty          $contact_clash_penalty 
chemical_score                 $chemical_score
energy_score                   $energy_score
energy_cutoff_distance         $energy_cutoff_distance
distance_dielectric            $distance_dielectric
dielectric_factor              $dielectric_factor
attractive_exponent            $attractive_exponent
repulsive_exponent             $repulsive_exponent
atom_model                     $atom_model 
vdw_scale                      $vdw_scale
electrostatic_scale            $electrostatic_scale
contact_minimize               $contact_minimize
chemical_minimize              $chemical_minimize
energy_minimize                $energy_minimize
initial_translation            $initial_translation
initial_rotation               $initial_rotation
initial_torsion                $initial_torsion
maximum_iterations             $maximum_iterations
contact_convergence            $contact_convergence
chemical_convergence           $chemical_convergence
energy_convergence             $energy_convergence
maximum_cycles                 $maximum_cycles
ligand_atom_file               ${ligand_number}.mol2
receptor_site_file             $HOME/dock_inputs_ece/${receptor_site_file}
score_grid_prefix              $HOME/dock_inputs_ece/${OS}_${score_grid_prefix}
vdw_definition_file            vdw.defn
chemical_definition_file       chem.defn
chemical_score_file            chem_score.tbl
flex_definition_file           flex.defn
flex_drive_file                flex_drive.tbl
ligand_contact_file            dock_cnt.mol2
ligand_chemical_file           dock_chm.mol2
ligand_energy_file             dock_nrg.mol2
automated_matching             $automated_matching
