Difference between revisions of "2016 DOCK tutorial with Beta Trypsin"

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Line 38: Line 38:
Minimization Input file: min.in
Minimization Input file: min.in
  conformer_search_type                                 rigid
  conformer_search_type                                       rigid
  use_internal_energy                                       yes
  use_internal_energy                                         yes
  internal_energy_rep_exp                               12
  internal_energy_rep_exp                                     12
  ligand_atom_file                                            ../01.dockprep/1bju.lig.mol2
  ligand_atom_file                                            ../01.dockprep/1BJU.lig.mol2
  limit_max_ligands                                           no
  limit_max_ligands                                           no
  skip_molecule                                                no
  skip_molecule                                                no
  read_mol_solvation                                       no
  read_mol_solvation                                           no
  calculate_rmsd                                              yes
  calculate_rmsd                                              yes
  use_rmsd_reference_mol                               yes
  use_rmsd_reference_mol                                       yes
  rmsd_reference_filename                             ../01.dockprep/1bju.lig.mol2
  rmsd_reference_filename                                     ../01.dockprep/1BJU.lig.mol2
  use_database_filter                                       no
  use_database_filter                                         no
  orient_ligand                                                 no
  orient_ligand                                               no
  bump_filter                                                     no
  bump_filter                                                 no
  score_molecules                                           yes
  score_molecules                                             yes
  contact_score_primary                                 no
  contact_score_primary                                       no
  contact_score_secondary                             no
  contact_score_secondary                                     no
  grid_score_primary                                       yes
  grid_score_primary                                           yes
  grid_score_secondary                                   no
  grid_score_secondary                                         no
  grid_score_rep_rad_scale                             1
  grid_score_rep_rad_scale                                     1
  grid_score_vdw_scale                                   1
  grid_score_vdw_scale                                         1
  grid_score_es_scale                                       1
  grid_score_es_scale                                         1
  grid_score_grid_prefix                                 ../03.box-grid/1bju.grid
  grid_score_grid_prefix                                       ../03.box-grid/1BJU.grid
  multigrid_score_secondary                         no
  multigrid_score_secondary                                   no
  dock3.5_score_secondary                           no
  dock3.5_score_secondary                                     no
  continuous_score_secondary                                  no
  continuous_score_secondary                                  no
  footprint_similarity_score_secondary                        no
  footprint_similarity_score_secondary                        no
Line 86: Line 86:
  flex_defn_file                                              ../zzz.parameters/flex.defn
  flex_defn_file                                              ../zzz.parameters/flex.defn
  flex_drive_file                                              ../zzz.parameters/flex_drive.tbl
  flex_drive_file                                              ../zzz.parameters/flex_drive.tbl
  ligand_outfile_prefix                                        1bju.min
  ligand_outfile_prefix                                        1BJU.min
  write_orientations                                          no
  write_orientations                                          no
  num_scored_conformers                                        1
  num_scored_conformers                                        1

Revision as of 13:43, 25 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.

I. Introduction

Yaping She & Omar Sanchez Reyes


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

Grid computing

V. Docking a Single Molecule for Pose Reproduction

Agatha Lyczek & Haoyue Guo


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

Rigid docking

Flexible Docking

VI. Virtual Screening

Katie Maffucci

DOCK Preparation

Post Processing

VIII. Frequently Encountered Problems