Batch High Throughput Virtual Screening Script

Rachit Mukkamala

Version 2.0

Description

A Bash script to submit batch jobs to ORCA, OpenBabel, MGLTools, and Autodock Vina. Automatically checks for syntax errors in ORCA input files, and can also identify ORCA runtime crashes. Provides a list of failed ORCA jobs at the end for easy troubleshooting. Organizes log files into individual directories, and creates an easy to read results summary text file. Created by Rachit Mukkamala

Prerequisite Installations

In order for the script to work, the following softwares must be installed:

• ORCA (https://orcaforum.kofo.mpg.de/app.php/portal)
• OpenBabel (https://open-babel.readthedocs.io/en/latest/Installation/install.html)
• MolKit Python Package (https://packages.ubuntu.com/source/xenial/mgltools-molkit)
• Autodock Vina (http://vina.scripps.edu/)
• Python 2.7 (https://www.python.org/download/releases/2.7/)

Params

The htvs_params.txt file specifies the full path to ORCA, the preferred ORCA input header for input file syntax checking, the path to MGLTools' prepare_ligand4.py script, the path to the Autodock Vina params script, and the path to the receptor protein. The params file can be renamed to whatever you prefer, however its contents must follow the format shown below:

PATH: /bin/the/path/to/orca
HEADER: ! B3LYP OPT def2-SVP NormalPrint Grid4 NormalSCF PAL2
MGL: prepare_ligand4.py
VINA: vina_params.txt
RECEPTOR: receptor_name.pdbqt

• If your ORCA is added to the $PATH environment variable and if you are not using OpenMPI, then for the PATH: row in batch_orca_params you can just write orca. Otherwise, make sure you write out the full path to ORCA. OpenMPI will only run if you write out the full ORCA path!
• Enter the entire desired ORCA header into the HEADER: row. If you are running a geometry optimization with DFT, B3LYP functional, and OpenMPI parallel processing, you can just copypaste the example header into the batch_orca_params.txt file.
• Enter the path to the MGLTools prepare-ligand.py script into the MGL: row.
• Enter the filename and/or path for the Autodock Vina config/params file into the VINA: row.
• Enter the filename and/or path for the receptor protein PDBQT file into the RECEPTOR: row.

Recommended File Structure

[root directory]
      htvs.sh
      htvs_params.txt
      prepare_ligand4.py
      [receptor].pdbqt
      vina_params.txt
      [input file directory]
          file1.inp
          file2.inp
          file3.inp
          [...].inp

Running the script

1. Set up the file structure outlined above
2. Provide execution privileges to the script by typing the command chmod +x htvs.sh
3. Recommended: If running using nohup: It is recommended that you run the script using nohup as follows: nohup bash htvs.sh [directory with input files] htvs_params.txt > [log.out] &
4. For conventional use: The script can also be run without nohup as follows. The only caveat is that all the script's messages will be sent to stdout and may be lost: ./htvs.sh [directory with input files] htvs_params.txt &

Citation

Please acknowledge use of this script in any paper/report as follows:

Mukkamala, R (2021) Batch High Throughput Virtual Screening Script (Version 1.0) [Source code].https://github.com/RackS103/Batch-HTVS

Attached below is the BibTex citation for this script for citation managers

@misc{mukkamala_2021, 
      title={Batch High Throughput Virtual Screening Script}, 
      url={https://github.com/RackS103/Batch-HTVS}, 
      publisher={GitHub}, 
      author={Mukkamala, Rachit}, 
      year={2021}, 
      month={Mar}
}

Please also acknowledge these other programs which are used by this script:

• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91
• Neese, F. (2012) The ORCA program system, Wiley Interdiscip. Rev.: Comput. Mol. Sci., 2, 73-78.
• N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. DOI:10.1186/1758-2946-3-33
• O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461