DOCK DN Parameters

Parameter	Description	Default
conformer_search_type	Choose between flex, rigid, denovo, or genetic	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_sidechain_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
dn_graph_max_picks	The number of fragment picks per layer per Dummy atom	30
dn_graph_breadth	The number of fragments chosen that are similar to successful fragment through Tanimoto	3
dn_graph_depth	The number of fragments choosen that are similar to successful fragments through Tanimoto	2
dn_graph_temp	The beginning annealing temperature	100.0
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	550
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	1
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	25
dn_max_layer_size	The number of partially grown molecules that advance through the search to subsequent attachment points	25
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