2017 DOCK tutorial 1 with PDB 4QMZ NEW

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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 a subsection of the AMS 536 class of 2017, using DOCK v6.8.

I. Introduction


DOCK is a molecular docking program used in drug discovery. It was developed by Irwin D. Kuntz, Jr. and colleagues at UCSF (see UCSF DOCK). This program, given a protein binding site and a small molecule, tries to predict the correct binding mode of the small molecule in the binding site, and the associated binding energy. Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug. DOCK works well as a screening procedure for generating leads, but is not currently as useful for optimization of those leads.

DOCK 6 uses an incremental construction algorithm called anchor and grow. It is described by a three-step process:

  1. Rigid portion of ligand (anchor) is docked by geometric methods.
  2. Non-rigid segments added in layers; energy minimized.
  3. The resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations.


In this tutorial we will use PDB code 4QMZ, the deposited crystal structure of MST3 in complex with SUNITINIB.

Organizing Directories

While performing docking, it is convenient to adopt a standard directory structure / naming scheme, so that files are easy to find / identify.For this tutorial, we will use something similar to the following:


In addition, most of the important files that are derived from the original crystal structure will be given a prefix that is the same as the PDB code, '4QMZ'. The following sections in this tutorial will adhere to this directory structure/naming scheme.

II. Preparing the Receptor and Ligand

Download the PDB file (4QMZ)

4QMZ was moved into 00.files

4qmz.pdb was copied to raw_4qmz.pdb

raw_4qmz.pdb was opened with VI terminal editor

    The header information, connect records, ions (atoms 2333 and 2334) and waters were deleted
    Res 178 = TPO, or phosphonothreonine
    Res 178 (TPO) was renamed to THR (Threonine) and HETATM renamed to ATOM, in addition the acanonical atoms were removed from the pdb leaving a deprotonated threonine (Atoms 1311-1314 in 4qmz.pdb)
    Res B49 was renamed to LIG and made Chain B

raw_4qmz.pdb was copied twice to 4qmz_rec.pdb and 4qmz_lig.pdb

4qmz_rec.pdb was opened with VI terminal editor

    LIG atoms, or chain B, was deleted and the file saved

4qmz_lig.pdb was opened with VI terminal editor

    Protein atoms, or chain A, was deleted and the file saved

4qmz_rec.pdb was loaded into tleap as a quality control measure

    source leaprc.protein.ff14SB
    lin = loadpdb /path/to/4qmz_rec.pdb
         2340 Hydrogens added, 1 heavy atom added (CSER RES 299, Chain A, OXT 12) 
    check lin
    saveamberparm lin /path/to/4qmz_rec_leap.parm7 /path/to/4qmz_rec_leap.crd

Running the receptor through leap ensures a reasonable starting structure and can help identify obvious issues sooner rather than later.

At this point the .parm7 and .crd have been created via tleap ambpdb can be used to obtain the clean pdb 4qmz_rec_leap.pdb

    ambpdb -p 4qmz_rec_leap.parm7 -c 4qmz_rec_leap.crd > 4qmz_rec_leap.pdb

Now add partial charges to the receptor and save file in .mol2 format:

    open chimera
    load 4qmz_rec_leap.pdb
    Tools --> Structure editing --> Add charge --> AMBER ff99SB with AM1-BCC charges 
    File --> Save Mol2... --> 4qmz.rec.mol2 

A no-hydrogen receptor pdb file will now be created:

    Chimera, load 4qmz.rec.mol2
    Select --> Chemistry --> element --> H
    Actions --> Atoms --> Delete
    File --> Save PDB... --> 4qmz.rec.noH.pdb

Ligand (4qmz_lig.pdb) will now be charged and saved in mol2 format

    open chimera
    load 4qmz_lig.pdb
    Tools --> structure editing --> AddH
    Tools --> Structure editing --> Add charge --> AMBER ff99SB with AM1-BCC charges 
    File --> Save mol2 --> 4qmz.lig.mol2

Placement of partial charges can be verified by examining the saved files 4qmz.lig.mol2 and 4qmz.rec.mol2.

III. Generating Receptor Surface and Spheres

Open 4qmz.rec.noH.pdb in Chimera

To generate the molecular surface:

  Action --> Surface --> Show

Save the .dms file

  Tools --> Structure editing --> write DMS

.dms save to 4qmz.rec.noH.dms

Create surface spheres

create input file INSPH


line 1 designates input file line 2 designates the generated spheres will be outside the receptor surface line 3 designates that all points on the receptor will be used line 4 designates the maximum surface radius of the spheres line 5 designates the minimum surface radius of the spheres line 6 designates the output file name

run sphgen

    sphgen -i INSPH -o OUTSPH

sphgen is the sphere generation program from dock -i desginates the input file: INSPH -o designates the output file

At this point it is beneficial to visualize the spheres that were created. This can be done with chimera: Open chimera from the terminal choose file --> open 4qmz.rec.mol2 choose file --> open 4qmz.rec.sph

The image that appears should resemble this:

Then we need to select the spheres pertinent to our docking experiment. Usually these speheres will be the closest N spheres to the native ligand molecule.


    sphere_selector 4qmz.rec.sph ../01.dockprep/4qmz.lig.mol2 8.0

This command will select all of the spheres within 8.0 angstroms of the ligand and output them to selected_spheres.sph

To visualize the spheres using Chimera as previously done: Launch Chimera, choose File -> Open, choose 4qmz.rec.noH.pdb File -> Open, choose output_spheres_selected.pdb Select -> Residue -> SPH Actions -> Atoms/Bonds -> sphere The selected spheres with the receptor surface should look similar to that as seen below:

IV. Generating Box and Grid

enter directory 03.box-grid

create input showbox.in


This input designates to dock that: we want to create a box the box length should be 8.0 Angstroms use the selected spheres in the file desginated output the box to the file specified

to use this input type:

    showbox < showbox.in

This box can be visualized in chimera using a similar approach as visualizing the spheres

Compute the energy grid

create grid.in file

    vi grid.in

grid.in needs to contain:

  compute_grids yes
  grid_spacing 0.4
  output_molecule no
  contact_score no
  energy_score yes
  energy_cutoff_distance 9999
  atom_model a
  attractive_exponent 6
  repulsive_exponent 12
  distance_dielectric yes
  dielectric_factor              4
  bump_filter yes
  bump_overlap 0.75
  receptor_file ../01.dockprep/4qmz.rec.mol2
  box_file ../03.box-grid/4qmz.box.pdb
  vdw_definition_file /opt/AMS536/dock6/parameters/vdw_AMBER_parm99.defn
  score_grid_prefix grid 

this script should output verbosely to the terminal and produce 2 output files, grid.bmp and grid.nrg, both binary files.

V. Docking a Single Molecule for Pose Reproduction

VI. Virtual Screening

VIII. Frequently Encountered Problems