Parameter List

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Parameter Description Default
conformer_search_type Choose between flex, rigid or denovo docking Flex
dn_fraglib_scaffold_file The path to the fragment library for just scaffolds
dn_fraglib_linker_file The path to the fragment library for just linkers
dn_fraglib_side_chain_file The path to the fragment library for just side chains
dn_user_specified_anchor Does the user have a specific anchor to use? Yes
dn_fraglib_anchor_file The path to the anchor .mol2 file
dn_use_torenv_table Will torsion environment be used? Yes
dn_torenv_table The path to the torsion environment (.dat)
dn_sampling_method Choose which method to use when choosing fragments for each layer (ex, random, graph) Graph
GRAPH: dn_graph_max_picks The number of fragment picks per layer per Dummy atom 30
GRAPH:dn_graph_breadth The number of fragments chosen that are similar to successful fragment through Tanimoto 3
GRAPH:dn_graph_depth The number of fragments choosen that are similar to successful fragments through Tanimoto 2
GRAPH:dn_graph_temp The beginning annealing temperature 100.0
RANDOM:dn_num_random_picks Number of fragments randomly chosen to add to anchor 20
dn_pruning_conformer_score_cutoff The max score allowed for fragment conformer addition to be accepted (kcal/mol) 100.0
dn_pruning_conformer_score_scaling_factor The weight put on the score cutoff 1.0
dn_pruning_clustering_cutoff The max score allowed post clustering 100.0
dn_constraint_mol_wt The max molecular weight allowed 1000.0
dn_constraint_rot_bon The max rotatable bonds allowed 15
dn_constraint_formal_charge Largest absolute charge of molecule 2.0
dn_heur_unmatched_num # of unmatched heavy atoms for hRMSD to be considered a different molecule when pruning between root and layer 1
dn_heur_matched_rmsd Max rmsd of matching heavy atoms of molecules to be considered similar molecule when pruning root to layer 2.0
dn_unique_anchors The number of unique anchors post clustering 3
dn_max_grow_layers Max numbers of layers that will be added to the anchor 9
dn_max_root_size The number of new anchors that seed the next layer of growth 100
dn_max_layer_size The number of partially grown molecules that advance through the search to subsequent attachment points 100
dn_max_current_aps Maximum attachment points the molecule can have at any one time (stop adding new scaffolds when the current fragment has this many open attachment points) 5
dn_max_scaffolds_per layer The max number of scaffolds added per layer per molecule 1
DN write checkpoints Write molecules for each layer Yes
DN write prune dump Write all molecules pruned out at every step No (lots of molecules)
DN write orients Write out the orients No
DN write growth trees Shows growth for every accepted molecule No
DN output prefix The name of the output file with final molecules output
Orient orient ligand If the anchor/ligand is in the binding pose orienting isn't necessary Yes
Orient Automated Matching The dock program will input the orient matching parameters (all default values) Yes
Orient Distance tolerance The tolerance in angstroms within which a pair of spheres is considered equivalent to

a pair of centers (Parameter used with automated matching for sphere selection)

Orient Distance minimum The minimum distance to be considered separate orients (avoid clustering) 2.0
Orient Nodes minimum The minimum number of heavy atoms to match for clustering 3
Orient Nodes Max The max number of heavy atoms to match to for clustering 10
Orient Receptor site file The selected spheres file
Orient Max orientations Max number of orients sampled 1000
Orient Critical points Used to focus initial anchor orientation into a subsite of the receptors active site. Spheres generated using sphgen deemed critical must be identified manually. (See Dock manual section 2.7.2 and 3.4.2 on Critical Points.) No
Orient Chemical Matching Aids anchor orientation based on chemical complementarity as defined in the chem_match.tbl file. Also must be done manually. (See Dock Manual section 2.7.3 and section 3.3.3 on Chemical Matching) No
Orient Use ligand spheres Use spheres generated from a ligand No