Parameter List

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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