Protein Target Preparation

Protein Target Preparation be-blasti is still the preferred method of downloading PDB files and splitting them into rec.pdb and xtal-lig.pdb files. Run it with

be_blasti.csh filename

The filename should be a file that contains PDB codes you want to download.

Once you get a rec.pdb (representing the protein) and xtal-lig.pdb (representing the ligand or a set of atoms in the binding site of the protein) (these names can be changed as well, see options), you can run blastermaster.py, the new version of DOCK Blaster. Try running the help to see the extensive options:

$DOCK_BASE/src/blastermaster_1.0/blastermaster.py  -h

A typical way of running it is to just run it as:

$DOCK_BASE/src/blastermaster_1.0/blastermaster.py -v

-v gives you verbose output, which can be helpful if something goes wrong. If everything is successful, you'll see this at the end of the file:

copying matching_spheres.sph into dockfiles
copying trim.electrostatics.phi into dockfiles
copying ligand.desolv.hydrogen into dockfiles
copying ligand.desolv.heavy into dockfiles
copying vdw.bmp into dockfiles
copying vdw.vdw into dockfiles
copying vdw.parms.amb.mindock into dockfiles
writing INDOCK file:  INDOCK

Otherwise something went wrong. Notice that you have an INDOCK file written for you, with many defaults set that you may want to change. Also, old INDOCK files are slightly incompatible with the new files, so you should consult the changed version written for you, or take a finer look at the page on the DOCK3.7 INDOCK file.

Adding Static Waters to the Protein Structure

Flexible Docking

Checking Your Protein Preparation

written by Reed Stein, 4/3/2019

Electrostatics

The electrostatics grid used in docking is called "trim.electrostatics.phi". This file contains the electrostatic potentials (in kT/e) in and around your protein structure, by solving the Poisson-Boltzmann equation using the program QNIFFT. The grid is trimmed to fit the DOCK box (called "box" in the working directory), which is overlaid onto your binding site. The input file for QNIFFT is called qnifft.parm, which reads in the "receptor.crg.lowdielectric.pdb" file, which contains your protein and low dielectric spheres, as well as your charge file "amb.crg.oxt" and radius file "vdw.siz". Your "receptor.crg.lowdielectric.pdb" file should have spheres that look like this:

  ATOM   9008  C   SPH  9008      87.491 136.887 124.980
  TER
  ATOM   9009  C   SPH  9009      87.900 138.214 123.837
  TER
  ATOM   9010  C   SPH  9010      88.222 138.764 124.234
  TER
  ATOM   9011  C   SPH  9011      88.080 138.630 124.390

For the QNIFFT calculation, the dielectric of the protein is set to 2, while the dielectric of anything outside the protein is 80, representing water. To check whether the atoms in your protein have been assigned the correct radii/charges after running QNIFFT, open the "qnifft.atm" output file. An example line from this file looks like this:

  ATOM      1  N   MET     1      84.419 139.350 124.664  1.65 -0.5200         N

where you have "ATOM", atom number, atom name, residue name, residue number, x coordinate, y coordinate, z coordinate, atomic radius, and atomic charge. The radius and charge values are taken from the "vdw.siz" and "amb.crg.oxt" files.

If you would like to manually run QNIFFT, run the following commands:

  $DOCKBASE/proteins/qnifft/bin/qnifft22_193_pgf_32 qnifft.parm
  $DOCKBASE/proteins/blastermaster/phiTrim.py qnifft.electrostatics.phi box trim.electrostatics.phi

The first command will generate the electrostatic potentials of the full protein. The second command requires the "box" file to trim the "qnifft.electrostatics.phi" to only fit inside the binding site box. This new output will be called "trim.electrostatics.phi".

To visualize your low dielectric sphere setup, open "receptor.crg.lowdielectric.pdb" in Chimera. Select all "SPH" residues and display/represent as spheres. Change the van der Waals radii of these spheres to the van der Waals "SPH" radius found in the "vdw.siz" file in your working directory. This line in the "vdw.siz" file should look like this:

   c     sph   1.90

To do this on the command line in Chimera, run the following commands:

   sel #0:SPH
   display sel
   represent sph sel
   vdwdefine 1.9 sel

The default radius is 1.90, but can be changed when scanning low dielectric sphere radii. To do this, change the radius in the "vdw.siz" file and then run QNIFFT again - see the tutorial on Parameter Scanning:

   http://wiki.docking.org/index.php/How_to_do_parameter_scanning

The actual electrostatic grids can be visualized by converting the "qnifft.electrostatics.phi" or "trim.electrostatics.phi" files into DX files for opening in Chimera. See the following tutorial for visualizing electrostatics grids:

   http://wiki.docking.org/index.php/Visualize_docking_grids

If you are happy with the way your spheres look, you can continue on to docking with them.

Ligand Desolvation

Heavy (radius = 1.8) and hydrogen (radius = 1.0) are generated in your working directory in "heavy/" and "hydrogen/", respectively. The input file for these two separate calculations is "INSEV", which looks like this:

   rec.crg.lds.pdb  ### receptor input file
   ligand.desolv.heavy ### grid you want to generate
   1.60,1.65,1.90,1.90,1.90,1.00  ## radii for O, N, C, S, P, X (other atom type)
   1.4 ### probe radius
   2 ### grid resolution
   box ### box file - determines the extent of grids to be calculated
   1.8 ### Born radius of atom - 1.8 for heavy, 1.0 for hydrogen

By default, the "rec.crg.lds.pdb" file does not have any spheres, i.e. "ligand desolvation spheres". However, if you include ligand desolvation spheres, e.g. when parameter scanning, spheres can be included with the atom name as "X" (different from "C" as in the low dielectric spheres), as shown below:

   ATOM   9008  X   SPH  9008      87.491 136.887 124.980
   TER
   ATOM   9009  X   SPH  9009      87.900 138.214 123.837
   TER
   ATOM   9010  X   SPH  9010      88.222 138.764 124.234
   TER
   ATOM   9011  X   SPH  9011      88.080 138.630 124.390
   

The "X" radius in the "INSEV" file can be changed so that different ligand desolvation grids with different sphere radii can be generated. To do this, change the radius in the "INSEV" files for both hydrogen and heavy ligand desolvation grids, then run Solvmap for both. These spheres can be visualized (same as above with low dielectric spheres) by opening the "rec.crg.lds.pdb" file in Chimera, selecting all "SPH" residues, representing them as spheres and setting the vdW radius to the value that corresponds to "X" in the INSEV file.

Solvmap needs to be run twice to generate the heavy and hydrogen ligand desolvation grids. To run Solvmap, you need the "rec.crg.lds.pdb" and "box" files, and then run the command:

   $DOCKBASE/proteins/solvmap/bin/solvmap >& solvmap.log

More advanced methods to alter your spheres, as well as increasing/decreasing charges on specific atoms can be found in these tutorials:

   http://wiki.docking.org/index.php/Using_thin_spheres_in_DOCK3.7
   http://wiki.docking.org/index.php/DOCK_3.7_tart

http://i.creativecommons.org/l/by-sa/3.0/88x31.png

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at https://sites.google.com/site/dock37wiki/.