Difference between revisions of "2016 DOCK tutorial with Beta Trypsin"
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Monaf Awwa | Monaf Awwa | ||
=== Box Generation=== | === Box Generation=== | ||
| + | First, open Chimera and open the RECEPTOR files 1BJU.rec.noH.pdb | ||
| + | Next, select the ACTION subheader, then select SURFACE, then SHOW | ||
| + | Once you can see the van der Waals surface of the protein, select the | ||
| + | TOOLS subheader, then STRUCTURE EDITING, and lastly select WRITE DMS and save the file as 1BJU.dms | ||
| + | Now that we have a surface, we can more effectively calculate regions of the protein where a small molecule can bind. To further accelerate calculations, we will specify which atoms to calculate the interactions for via the program sphgen | ||
| + | === Grid computing=== | ||
| + | first, create an input file for sphgen to read. | ||
| − | + | vim INSPH | |
| + | The file should have the following information. Remember that | ||
==V. Docking a Single Molecule for Pose Reproduction== | ==V. Docking a Single Molecule for Pose Reproduction== | ||
Revision as of 14:10, 26 March 2016
For additional Rizzo Lab tutorials see DOCK Tutorials. Use this link Wiki Formatting as a reference for editing the wiki. This tutorial was developed collaboratively by the AMS 536 class of 2014, using DOCK v6.6.
Contents
I. Introduction
Yaping She & Omar Sanchez Reyes
DOCK
Beta Trypsin
Organizing Directories
II. Preparing the Receptor and Ligand
Beilei Jiang
III. Generating Receptor Surface and Spheres
Lauren Prentis
Generating the Receptor Surface
Placing Spheres
IV. Generating Box and Grid
Monaf Awwa
Box Generation
First, open Chimera and open the RECEPTOR files 1BJU.rec.noH.pdb Next, select the ACTION subheader, then select SURFACE, then SHOW
Once you can see the van der Waals surface of the protein, select the TOOLS subheader, then STRUCTURE EDITING, and lastly select WRITE DMS and save the file as 1BJU.dms
Now that we have a surface, we can more effectively calculate regions of the protein where a small molecule can bind. To further accelerate calculations, we will specify which atoms to calculate the interactions for via the program sphgen
Grid computing
first, create an input file for sphgen to read.
vim INSPH
The file should have the following information. Remember that
V. Docking a Single Molecule for Pose Reproduction
Agatha Lyczek & Haoyue Guo
Minimization
Dock Minimization Input file: min.in
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 12 ligand_atom_file ../01.dockprep/1BJU.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../01.dockprep/1BJU.lig.mol2 use_database_filter no orient_ligand no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../03.box-grid/1BJU.grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no ph4_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_descriptor_score_secondary no amber_score_secondary no minimize_ligand yes simplex_max_iterations 1000 simplex_tors_premin_iterations 0 simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10.0 atom_model all vdw_defn_file ../zzz.parameters/vdw.defn flex_defn_file ../zzz.parameters/flex.defn flex_drive_file ../zzz.parameters/flex_drive.tbl ligand_outfile_prefix 1BJU.min write_orientations no num_scored_conformers 1 rank_ligands no
Result:
Rigid docking
To run the input file:
dock6 -i rigid_nr.in
Rigid docking input file: rigid_nr.in
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 12 ligand_atom_file ../01.dockprep/1BJU.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../01.dockprep/1BJU.lig.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../02.surface-sphere/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../03.box-grid/1BJU.grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no ph4_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_descriptor_score_secondary no amber_score_secondary no minimize_ligand yes simplex_max_iterations 1000 simplex_tors_premin_iterations 0 simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_random_seed 0 simplex_restraint_min yes atom_model all vdw_defn_file ../zzz.parameters/vdw.defn flex_defn_file ../zzz.parameters/flex.defn flex_drive_file ../zzz.parameters/flex_drive.tbl ligand_outfile_prefix 1BJU.rigid_nr write_orientations no
Best scored rigid docking result:
Flexible Docking
To run the input file:
dock6 -i flex.in
Flexible docking input file: flex.in
conformer_search_type flex user_specified_anchor no limit_max_anchors no min_anchor_size 5 pruning_use_clustering yes pruning_max_orients 1000 pruning_clustering_cutoff 100 pruning_conformer_score_cutoff 100.0 use_clash_overlap no write_growth_tree no use_internal_energy yes internal_energy_rep_exp 12 ligand_atom_file ../01.dockprep/1BJU.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../01.dockprep/1BJU.lig.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../02.surface-sphere/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../03.box-grid/1BJU.grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no ph4_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_descriptor_score_secondary no amber_score_secondary no minimize_ligand yes minimize_anchor yes minimize_flexible_growth yes use_advanced_simplex_parameters no simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0
Best scored flexible docking result:
VI. Virtual Screening
Katie Maffucci
DOCK Preparation
Post Processing
VIII. Frequently Encountered Problems
EVERYONE
