DOCK 3.7 parameter ##################################################### # NOTE: split_database_index is reserved to specify a list of files ligand_atom_file split_database_index ##################################################### # OUTPUT output_file_prefix test. ##################################################### # MATCHING match_method 2 distance_tolerance 0.05 match_goal 5000 distance_step 0.05 distance_maximum 0.5 timeout 10.0 nodes_maximum 4 nodes_minimum 4 bump_maximum 10.0 bump_rigid 10.0 ##################################################### # COLORING chemical_matching no case_sensitive no ##################################################### # SEARCH MODE atom_minimum 4 atom_maximum 100 number_save 1 number_write 1 molecules_maximum 100000 check_clashes yes do_premax no do_clusters no ##################################################### # SCORING ligand_desolvation volume vdw_maximum 1.0e10 electrostatic_scale 1.0 vdw_scale 1.0 internal_scale 0.0 per_atom_scores no ##################################################### # DOCKovalent dockovalent no bond_len 1.8 bond_ang1 109.5 bond_ang2 109.5 len_range 0.0 len_step 0.1 ang1_range 10.0 ang2_range 10.0 ang1_step 2.5 ang2_step 2.5 ##################################################### # INPUT FILES / THINGS THAT CHANGE receptor_sphere_file ../dockfiles/matching_spheres.sph vdw_parameter_file ../dockfiles/vdw.parms.amb.mindock delphi_nsize 97 flexible_receptor no total_receptors 1 ############## grids/data for one receptor rec_number 1 rec_group 1 rec_group_option 1 solvmap_file ../dockfiles/ligand.desolv.heavy hydrogen_solvmap_file ../dockfiles/ligand.desolv.hydrogen delphi_file ../dockfiles/trim.electrostatics.phi chemgrid_file ../dockfiles/vdw.vdw bumpmap_file ../dockfiles/vdw.bmp ############## end of INDOCK