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_num	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