Fragment Library Generation

An example of an input file to generate a fragment library calling DOCK6:

conformer_search_type                                        flex
user_specified_anchor                                        no
limit_max_anchors                                            no
min_anchor_size                                              5
pruning_use_clustering                                       no
pruning_max_orients                                          100
pruning_orient_score_cutoff                                  100.0
pruning_max_conformers                                       75
pruning_conformer_score_cutoff                               100.0
use_clash_overlap                                            no
write_growth_tree                                            no
write_fragment_libraries                                     yes
fragment_library_prefix                                      ${SYSTEM}.fraglib
fragment_library_freq_cutoff                                 ${FREQ_CUTOFF}
fragment_library_sort_method                                 ${SORT_METHOD}
fragment_library_trans_origin                                no
use_internal_energy                                          no
ligand_atom_file                                             ../001.files/${SYSTEM}.lig.multigridmin.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                ../001.files/vdw.defn
flex_defn_file                                               ../001.files/flex.defn
flex_drive_file                                              ../001.files/flex_drive.tbl
ligand_outfile_prefix                                        output
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no