Parameter List

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)	0.25
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