README

General info

The whole test set is located at ${TESTSET_PATH}=/gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/.
The file bickel_denovo_systems.dat contains the 57 systems to be used in our tests.
The test set is divided in two parts, one containing 40 molecules and another containing 17. This is meant to paralelize our jobs in the rn-long-40core or long-40core nodes.

DOCK simulation files are contained in /gpfs/projects/rizzo/yuchzhou/RCR/DOCK_testset/${PDB}/zzz.dock_files/ where ${PDB} corresponds to each line of bickel_denovo_systems.dat.
- ${PDB}.lig.am1bcc.mol2 is the am1bcc charged ligand to be used as a reference.
- ${PDB}.lig.cartmin.mol2 is the cartesian minimized ligand to be used to produced footprints.
- ${PDB}.rec.clean.mol2 is the receptor mol2 file with hydrogen atoms.
- ${PDB}.rec.clust.close.sph is the file containing the spheres the simulation requires.
- ${PDB}.rec.nrg and ${PDB}.rec.bmp are the grid files
In order to avoid unnecessary copies, have your scripts point to these places instead of copies inside your project space.

Run the script below to generate 57 directories with their respective subdirectories and input files.

bash organize_systems.sh -i bickel_denovo_systems.dat

Make sure you read organize_systems.sh and change the scoring functions to whichever scoring functions you were assigned to calculate.
Using Python >=3, run the script below:

python3 create_slurm_scripts.py

Make sure that you have bickel_denovo_systems_40.dat and bickel_denovo_systems_17.dat in the directory where the script is located. The script generates a plethora of slurm scripts that can be submitted using a simple for-loop:

for elem in run*.sh; do echo ${elem}; sbatch ${elem}; done

When the simulations are done, make sure you run the following script to organize the analysis material:

bash analyze_results.sh bickel_denovo_systems.dat