Parameter List

Input_Parameter	Description	Default_value
conformer_search_type	Choose between flex, rigid, or denovo docking	Flex
dn_fraglib_scaffold_file	The path to the fragment library for just scaffold fragments
dn_fraglib_linker_file	The path to the fragment library for just linker fragments
dn_fraglib_sidechain_file	The path to the fragment library for just sidechain fragments
dn_user_specified_anchor	Does the user have a specific anchor to use with Dummy atom notated in the .mol2?	yes
dn_fraglib_anchor_file	The path to the anchor .mol2 file with attachment point notated as "Du"
dn_use_torenv_table	Will torsion environment table be used for checking bond connectivity?	yes
dn_torenv_table	The path to the torsion environment .dat file
dn_sampling_method	which method will be used to choose fragments for each layer: exhaustive (ex), random, or graph	graph
GRAPH: dn_graph_max_picks	The number of fragments chosen to add to the anchor per layer per attachment point(Du)
GRAPH: dn_graph_breadth	The number of fragments chosen that are similar to successful fragment in the row through Tanimoto similarity
GRAPH: dn_graph_depth	The number of fragments chosen that are similar to successful fragment in the column through Tanimoto similarity
GRAPH: dn_graph_temp	The beginning annealing temperature (usually 100 and scales down to one for each layer)	100
RANDOM: dn_num_random_picks	The number of fragments randomly chosen to add to each attachment point (Du)	20
dn_pruning_conformer_score_cutoffr	the max score allowed for each fragment conformer addition to be accepted (kcal/mol)	100.0
dn_pruning_conformer_score_sclaing_factor	The coefficient of 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 the molecule	2.0
dn_heur_unmatched_num	Tanimoto similarity*	1
dn_heur_matched_rmsd	The pruning cutoff for RMSD similarity	2.0
dn_unique_anchors	The number of unique anchors post clustering	3.0
dn_max_grow_layers	The max number of layers that will be added to the anchor	9.0
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	Currently unknown*	5
dn_max_scaffolds_per_layer	The max number of scaffolds added per layer per anchor	1
dn_write_checkpoints	Write molecules for each layer for each anchor	yes
dn_write_prune_dump	Write all molecules pruned out at every layer (lots of molecules)	no
dn_write_orients	Write out the orients into an orient file	no
dn_write_growth_trees	Shows growth at every layer for every accepted molecule	no
dn_output_prefix	The name of the output file with the final ensemble of molecules	output
ORIENT: orient_ligand	Do you want to orient the ligand (no if it's in the correct orientation prior to denovo)	yes

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	Tolerance (like sd/se?) ***needs to be edited	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