Example of an Input file

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This is a standard input file for de novo DOCK6 using multigrid score through descriptor score.

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     /PATH/gen-frags-12/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       /PATH/gen-frags-12/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    /PATH/gen-frags-12/fraglib_sidechain.mol2
dn_user_specified_anchor                                     yes
dn_fraglib_anchor_file                                       /PATH/01.files/anchor.mol2
dn_use_torenv_table                                          yes
dn_torenv_table                                              /PATH/gen-frags-12/fraglib_torenv.dat
dn_sampling_method                                           graph
dn_graph_max_picks                                           30
dn_graph_breadth                                             3
dn_graph_depth                                               2
dn_graph_temperature                                         100
dn_pruning_conformer_score_cutoff                            100.0
dn_pruning_conformer_score_scaling_factor                    2.0
dn_pruning_clustering_cutoff                                 100.0
dn_constraint_mol_wt                                         550
dn_constraint_rot_bon                                        15
dn_constraint_formal_charge                                  2.0
dn_heur_unmatched_num                                        1
dn_heur_matched_rmsd                                         2.0
dn_unique_anchors                                            1
dn_max_grow_layers                                           2
dn_max_root_size                                             25
dn_max_layer_size                                            25
dn_max_current_aps                                           5
dn_max_scaffolds_per_layer                                   1
dn_write_checkpoints                                         yes
dn_write_prune_dump                                          yes
dn_write_orients                                             no
dn_write_growth_trees                                        no
dn_output_prefix                                             final
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           /PATH/01.files/spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
footprint_similarity_score_primary                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    no
descriptor_use_multigrid_score                               yes
descriptor_use_pharmacophore_score                           no
descriptor_use_tanimoto                                      no
descriptor_use_hungarian                                     no
descriptor_use_volume_overlap                                no
descriptor_multigrid_score_rep_rad_scale                     1
descriptor_multigrid_score_vdw_scale                         1
descriptor_multigrid_score_es_scale                          1
descriptor_multigrid_score_number_of_grids                   14
descriptor_multigrid_score_grid_prefix0                      ../../07.multigrid/SYSTEM.resid_025
descriptor_multigrid_score_grid_prefix1                      ../../07.multigrid/SYSTEM.resid_028
descriptor_multigrid_score_grid_prefix2                      ../../07.multigrid/SYSTEM.resid_029
descriptor_multigrid_score_grid_prefix3                      ../../07.multigrid/SYSTEM.resid_032
descriptor_multigrid_score_grid_prefix4                      ../../07.multigrid/SYSTEM.resid_036
descriptor_multigrid_score_grid_prefix5                      ../../07.multigrid/SYSTEM.resid_092
descriptor_multigrid_score_grid_prefix6                      ../../07.multigrid/SYSTEM.resid_095
descriptor_multigrid_score_grid_prefix7                      ../../07.multigrid/SYSTEM.resid_096
descriptor_multigrid_score_grid_prefix8                      ../../07.multigrid/SYSTEM.resid_098
descriptor_multigrid_score_grid_prefix9                      ../../07.multigrid/SYSTEM.resid_099
descriptor_multigrid_score_grid_prefix10                     ../../07.multigrid/SYSTEM.resid_102
descriptor_multigrid_score_grid_prefix11                     ../../07.multigrid/SYSTEM.resid_103
descriptor_multigrid_score_grid_prefix12                     ../../07.multigrid/SYSTEM.resid_106
descriptor_multigrid_score_grid_prefix13                     ../../07.multigrid/SYSTEM.resid_remaining
descriptor_multigrid_score_fp_ref_mol                        yes
descriptor_multigrid_score_footprint_ref                     /PATH/01.files/lig.multigridmin.mol2
descriptor_multigrid_score_foot_compare_type                 Euclidean
descriptor_multigrid_score_normalize_foot                    no
descriptor_multigrid_score_vdw_euc_scale                     1.0
descriptor_multigrid_score_es_euc_scale                      1.0
descriptor_weight_multigrid_score                            1
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_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_grow_tors_premin_iterations                          0
simplex_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /PATH/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /PATH/dock6/parameters/flex.defn
flex_drive_file                                              /PATH/dock6/parameters/flex_drive.tbl