Protein Target Preparation Updated
Checking Your Protein Preparation
written by Reed Stein, 4/3/2019
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:
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:
If you are happy with the way your spheres look, you can continue on to docking with them.
Heavy (radius = 1.8) and hydrogen (radius = 1.0) ligand desolvation grids 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: