How to do parameter scanning

Manually Generating ES/LD Combinations

written by Reed Stein, 4/15/2019

To generate different sized low dielectric and ligand desolvation thin sphere combinations, you must first run blastermaster on your protein/ligand of interest. Once this is finished, make a new directory. Change into the new directory and run the following command:

    python ~rstein/zzz.scripts/DOCK_prep_scripts/0001_combined_ES_LD_generation.py {FULL_ORIGINAL_BLASTERMASTER_PATH} '0.5 1.0 1.5 1.9' 1.0 4

The arguments are:

   1) The full path of your original blastermaster directory, e.g. /mnt/nfs/work/asdf/asdf/asdf/blastermaster_prep
   2) Radius of ES/LD spheres you want to run. This needs to be in quotes, e.g. '0.5 0.7 1.0 1.5'
   3) Molecular surface density. The higher the number, the more dense the molecular surface is. 1.0 is recommended
   4) Maximum distance thin spheres should be from your xtal-lig.pdb. 2-4 Angstroms is a good choice. Default in blastermaster is 2.

This script will submit ligand desolvation jobs to the queue. This should take 15-30 minutes. Once finished, check your spheres and grids by following the steps here:

   http://wiki.docking.org/index.php?title=Protein_Target_Preparation

Then run the following script to combine the ES/LD grids in all combinations:

   python ~rstein/zzz.scripts/DOCK_prep_scripts/0002_combine_es_ld_grids_into_combos.py {FULL_ORIGINAL_BLASTERMASTER_PATH}

This will create a new directory called "combo_directories" with docking-ready directories inside. The directories will have the name "es_{ES_sphere_radius}_ld_{LD_sphere_radius}". "def" refers to grids taken from your {FULL_ORIGINAL_BLASTERMASTER_PATH} directory.

These directories are now ready for docking.

Blastermaster Parameter Scanning

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep 
                                                                |
                                                                |------ dockfiles
              |                                                 | 
              |                                                 |----- working
              |                                                 |
              |                                                 ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
              |
              ------- script ------ dockprep_thin_spheres_in_batches.csh
                              |
                              |------ submit_dockprep_thin_spheres.csh
                              |
                              |------ dockprep_thin_spheres.csh
                              |
                              |------ lig-decoy_enrichment.csh
                              |
                              |------ combineScoresAndPoses.csh
                              |
                              |------ AUCplot_of-lig-decoys.csh
                              |
                              |------ mk_matrix_logAUC.py
                              |
                              |------ sph_lib.py
                              |
                              |------ pdb_lib.py
                              |
                              ------- close_sph.py

1) Make those directories above.

mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory

cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path, and modify as necessary.

cd script

cp /mnt/nfs/ex5/work/jklyu/large_scale_docking/DRD2/struct_20180322/A122I_add_polarH_mini_HID/thin_spheres_parameter_scanning/scripts/*dockprep* .

cp /mnt/nfs/reshwork/jklyu/D2R/scripts/lig-decoy_enrichment_submit.csh .
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/combineScoresAndPoses.csh .
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/reshwork/jklyu/D2R/scripts/mk_matrix_logAUC.py .

5) Run parameter scanning.

cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

  mkdir ligands-decoys
  cd ligands-decoys
  mkdir ligands
  mkdir decoys

now copy your decoys.db2.gz to decoys now copy your ligands.db2.gz to ligands now copy decoys.smi to the folder now copy ligands.smi to the folder

7) Submit DOCK and enrichment calculation.

csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.

csh /path/to/script/combineScoresAndPoses.csh #1st change the path inside the script to your own dir
csh /path/to/script/AUCplot_of-lig-decoys.csh #1st change the path inside the script to your own dir

9) Visualize the logAUC by heatmap.

python /path/to/script/mk_matrix_logAUC.py