Difference between revisions of "Parameter List"

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|dn_max_scaffolds_per layer
|The max number of scaffolds added per layer per molecule
|The max number of scaffolds added per layer per molecule

Revision as of 14:29, 8 January 2018

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_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
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)

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