Difference between revisions of "Parameter List"
From Rizzo_Lab
Stonybrook (talk | contribs) |
Stonybrook (talk | contribs) |
||
| Line 118: | Line 118: | ||
|1 | |1 | ||
|- | |- | ||
| − | | | + | |dn_write_checkpoints |
|Write molecules for each layer | |Write molecules for each layer | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |dn_write_prune_dump |
|Write all molecules pruned out at every step | |Write all molecules pruned out at every step | ||
|No (lots of molecules) | |No (lots of molecules) | ||
|- | |- | ||
| − | | | + | |dn_write_orients |
|Write out the orients | |Write out the orients | ||
|No | |No | ||
|- | |- | ||
| − | | | + | |dn_write_growth_trees |
|Shows growth for every accepted molecule | |Shows growth for every accepted molecule | ||
|No | |No | ||
|- | |- | ||
| − | | | + | |dn_output_prefix |
|The name of the output file with final molecules | |The name of the output file with final molecules | ||
|output | |output | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> orient_ligand |
|If the anchor/ligand is in the binding pose orienting isn't necessary | |If the anchor/ligand is in the binding pose orienting isn't necessary | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> automated_matching |
|The dock program will input the orient matching parameters (all default values) | |The dock program will input the orient matching parameters (all default values) | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> distance_tolerance |
|The tolerance in angstroms within which a pair of spheres is considered equivalent to | |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) | a pair of centers (Parameter used with automated matching for sphere selection) | ||
|0.25 | |0.25 | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> distance_minimum |
|The minimum distance to be considered separate orients (avoid clustering) | |The minimum distance to be considered separate orients (avoid clustering) | ||
|2.0 | |2.0 | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> nodes_minimum |
|The minimum number of heavy atoms to match for clustering | |The minimum number of heavy atoms to match for clustering | ||
|3 | |3 | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> nodes_max |
|The max number of heavy atoms to match to for clustering | |The max number of heavy atoms to match to for clustering | ||
|10 | |10 | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> receptor_site_file |
|The selected spheres file | |The selected spheres file | ||
| | | | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> max_orientations |
|Max number of orients sampled | |Max number of orients sampled | ||
|1000 | |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.) | |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 | |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) | |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 | |No | ||
|- | |- | ||
| − | | | + | |<span style="font-weight:bold">ORIENT:</span> use_ligand_spheres |
|Use spheres generated from a ligand | |Use spheres generated from a ligand | ||
|No | |No | ||
|} | |} | ||
Revision as of 12:29, 16 May 2017
| 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_side_chain_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) |
0.25 |
| 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 |
