Difference between revisions of "How to do parameter scanning"

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now copy your decoys.db2.gz to decoys
 
now copy your decoys.db2.gz to decoys
 
now copy your ligands.db2.gz to ligands
 
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.
 
7) Submit DOCK and enrichment calculation.

Revision as of 12:13, 9 February 2017

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.

cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/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