Removing Spheres (The Chase Method)

These scripts are used for removing ligand desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way.

5/21/2020 Pioneered by Chase Webb. Scripts written by Reed Stein.

The first script requires that you have already run blastermaster and have a directory containing the "working/" subdirectory containing the "receptor.crg.lowdielectric.pdb" file. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.

    python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404

If you want to include more atom coordinates, include more x,y,z coordinates.

    python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 58.038 47.323 12.300

To increase the radius around the atoms that you want to remove ligand desolvation spheres from, include the -d flag:

   python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_remove_spheres.py -p {YOUR_DOCK_DIR} -c 42.301 43.502 48.404 -d 5

Once you have run this script, you can visualize your spheres by following this tutorial:

   http://wiki.docking.org/index.php/Protein_Target_Preparation_Updated#Checking_Your_Protein_Preparation

If satisfied with your spheres, run the second script to recalculate the "hydrogen" and "heavy" ligand desolvation grids. This script submits the SOLVMAP calculation to the queue. It requires the radius of your ligand desolvation spheres for the SOLVMAP calculation. As before you need the "working/" subdirectory containing the "box" file and the newly created "rec.crg.lds.pdb" file from the previous script. If you already have "hydrogen/" and "heavy/" subdirectories within your "working/" directory, it will ask you to either move or delete these.

If you had a ligand desolvation sphere radius of 0.1 Å, use the following command:

  python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_make_ld_dirs.py -p {YOUR_DOCK_DIR} -r 0.1

FINAL STEP! Once you have generated the "ligand.desolv.hydrogen" and "ligand.desolv.heavy" grids in {YOUR_DOCK_DIR/working/hydrogen/ and {YOUR_DOCK_DIR/working/heavy/ directories, make sure to copy them to your "/dockfiles/" directory:

   cp {YOUR_DOCK_DIR/working/hydrogen/ligand.desolv.hydrogen dockfiles/.
   cp {YOUR_DOCK_DIR/working/heavy/ligand.desolv.heavy dockfiles/.