| DOCK 3.7 parameter |
| ##################################################### |
| # NOTE: split_database_index is reserved to specify a list of files |
| # defults for large scale docking. |
| 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 100 |
| bump_rigid 100 |
| mol2_score_maximum -10.0 |
| ##################################################### |
| # COLORING |
| chemical_matching no |
| case_sensitive no |
| ##################################################### |
| # SEARCH MODE |
| atom_minimum 4 |
| atom_maximum 100 |
| number_save 1 |
| number_write 1 |
| flush_int 100 |
| #molecules_maximum 100000 |
| check_clashes yes |
| do_premax no |
| do_clusters no |
| ##################################################### |
| # SCORING |
| ligand_desolvation volume |
| #vdw_maximum 1.0e10 |
| ligand_desolv_scale 1.0 |
| 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 |
| ##################################################### |
| # MINIMIZATION |
| minimize yes |
| sim_itmax 500 |
| sim_trnstep 0.2 |
| sim_rotstep 5.0 |
| sim_need_to_restart 1.0 |
| sim_cnvrge 0.1 |
| min_cut 1.0e15 |
| iseed 777 |
| ##################################################### |
| # INPUT FILES / THINGS THAT CHANGE |
| receptor_sphere_file ../dockfiles/matching_spheres.sph |
| vdw_parameter_file ../dockfiles/vdw.parms.amb.mindock |
| delphi_nsize 63 |
| 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 |
|
|
