Difference between revisions of "Parameter List"

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|-
 
|-
 
| conformer_search_type
 
| conformer_search_type
−
| Choose between flex, rigid or denovo docking
+
| Choose between flex, rigid, denovo, or genetic
 
| Flex
 
| Flex
 
|-
 
|-
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|
 
|
 
|-
 
|-
−
|dn_fraglib_side_chain_file
+
|dn_fraglib_sidechain_file
 
|The path to the fragment library for just side chains
 
|The path to the fragment library for just side chains
 
|
 
|
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|Graph
 
|Graph
 
|-
 
|-
−
|<span style="font-weight:bold">GRAPH:</span> dn_graph_max_picks  
+
| dn_graph_max_picks  
 
|The number of fragment picks per layer per Dummy atom
 
|The number of fragment picks per layer per Dummy atom
 
|30
 
|30
 
|-
 
|-
−
|<span style="font-weight:bold">GRAPH:</span>dn_graph_breadth
+
| dn_graph_breadth
 
|The number of fragments chosen that are similar to successful fragment through Tanimoto
 
|The number of fragments chosen that are similar to successful fragment through Tanimoto
 
|3
 
|3
 
|-
 
|-
−
|<span style="font-weight:bold">GRAPH:</span>dn_graph_depth
+
| dn_graph_depth
 
|The number of fragments choosen that are similar to successful fragments through Tanimoto
 
|The number of fragments choosen that are similar to successful fragments through Tanimoto
 
|2
 
|2
 
|-
 
|-
−
|<span style="font-weight:bold">GRAPH:</span>dn_graph_temp
+
| dn_graph_temp
 
|The beginning annealing temperature  
 
|The beginning annealing temperature  
 
|100.0
 
|100.0
 
|-
 
|-
−
|<span style="font-weight:bold">RANDOM:</span>dn_num_random_picks
+
| dn_num_random_picks
 
|Number of fragments randomly chosen to add to anchor
 
|Number of fragments randomly chosen to add to anchor
 
|20
 
|20
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|dn_constraint_mol_wt
 
|dn_constraint_mol_wt
 
|The max molecular weight allowed  
 
|The max molecular weight allowed  
−
|1000.0
+
|550
 
|-
 
|-
 
|dn_constraint_rot_bon
 
|dn_constraint_rot_bon
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|dn_unique_anchors
 
|dn_unique_anchors
 
|The number of unique anchors post clustering
 
|The number of unique anchors post clustering
−
|3
+
|1
 
|-
 
|-
 
|dn_max_grow_layers
 
|dn_max_grow_layers
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|dn_max_root_size
 
|dn_max_root_size
 
|The number of new anchors that seed the next layer of growth
 
|The number of new anchors that seed the next layer of growth
−
|100
+
|25
 
|-
 
|-
 
|dn_max_layer_size  
 
|dn_max_layer_size  
 
|The number of partially grown molecules that advance through the search to subsequent attachment points
 
|The number of partially grown molecules that advance through the search to subsequent attachment points
−
|100
+
|25
 
|-
 
|-
 
|dn_max_current_aps
 
|dn_max_current_aps
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|5
 
|5
 
|-
 
|-
−
|dn_max_scaffolds_per layer
+
|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
 
|1
 
|1
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|output
 
|output
 
|-
 
|-
−
|<span style="font-weight:bold">ORIENT:</span> orient_ligand
+
 
−
|If the anchor/ligand is in the binding pose orienting isn't necessary
 
−
|Yes
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> automated_matching
 
−
|The dock program will input the orient matching parameters (all default values)
 
−
|Yes
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> 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)
 
−
|0.25
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> distance_minimum
 
−
|The minimum distance to be considered separate orients (avoid clustering)
 
−
|2.0
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> nodes_minimum
 
−
|The minimum number of heavy atoms to match for clustering
 
−
|3
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> nodes_max
 
−
|The max number of heavy atoms to match to for clustering
 
−
|10
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> receptor_site_file
 
−
|The selected spheres file
 
−
|
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> max_orientations
 
−
|Max number of orients sampled
 
−
|1000
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> 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
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> 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
 
−
|-
 
−
|<span style="font-weight:bold">ORIENT:</span> use_ligand_spheres
 
−
|Use spheres generated from a ligand
 
−
|No
 
 
|}
 
|}

Latest revision as of 10:43, 25 January 2019

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
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