Preparing the ATG Primary Screen

After the ATG Prescreen has been post-processed, we can prepare the ATG Primary Screen:

1. Todo File: Creation of one or more todo files for the ATG Primary Screens. One todo file is created for each screening size that is passed to the command. For the preparation of this file, the Sparse Metrics Files are needed that were created in the section Postprocessing the ATG Prescreen.

2. VFVS Folder: Preparation of a new VFVS folder for the ATG Primary Screen

3. Input Files: The VFVS Folder needs to be prepared by copying the docking input files into it, as well as the todo file that contains the ligand collections that should be screened. In addition, the all.ctrl file has to be configured with the proper settings.

Now we can run the script that carries out steps 1-3 from above automatically, which can be done by running the following command in the tools folder:

./vfvs_prepare_atg-primary-screen.sh gk-vs1 10000

The first argument is a prefix that can be freely chosen, that is used for the file path when the screening data is stored in S3. We chose the prefix gk-vs1, "gk" referring to the target glucokinase, and "vs1" for virtual screening 1. The screening size specified here has to match with the screening size that was specified during the postprocessing of the ATG Prescreen ( Postprocessing the ATG Prescreen).

For each docking scenario and each specified screening size, a new VFVS folder was created in the parent folder ../../ (two levels above the current working directory), one for each ATG Primary Screen. In our case, we have one docking scenario called gk_ds1. We now change the directory to the corresponding ATG primary screen folder:

cd ../../atg-primary_10000_gk-ds1/tools

Then we prepare the workflow in the same way as we did for the ATG Prescreen:

./vfvs_prepare_folders.py
./vfvs_prepare_workunits.py
./vfvs_build_docker.sh

The command ./vfvs_prepare_workunits.py will print the total number of work units. Please remember this number, as it is needed in the next section.