Prepare receptor and ligand files for docking using Python scripts

Docking software such as Autodock4 [1] and Autodock Vina [2] require input receptor and ligand files in a specific format called pdbqt. Sometimes, preparing files using Autodock Tools (ADT) gives various errors that are not easily understandable. Especially, when we are performing virtual screening (VS), we need to convert a lot of files from pdb to pdbqt format. Converting each file one by one using ADT is a tedious job. Therefore, python scripts provided by Autodock are quite helpful.

In this article, we will prepare the input receptor and ligand docking files using Python scripts.

1. Preparing Ligands

At first, locate the ‘prepare_ligand.py’ (or ‘prepare_ligand4.py’ for Autodock4) file in the MGLTools directory you have already installed. The script will be present in /path/to/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/ or download from here or here.

Keep your ligands in a directory in pdb format and run this script as follows:

$ python prepare_ligand.py -l ligand.pdb -v -o ligand.pdbqt

Here, -l defines the ligand filename, -o is the output file, and -v is for displaying processing (default is minimal output).

There are other arguments that you can define such as

• -d dictionary to write types list and number of active torsions “
• -A type(s) of repairs to make:\n\t\t bonds_hydrogens, bonds, hydrogens (default is to do no repairs)”
• -B type(s) of bonds to allow to rotate.
• -M interactive (default is automatic output), and so on.

To know more options, type $ python prepare_ligand.py -h.

You can set parameters for the first ligand PDB file and then use the same command for all ligand files.

2. Prepare receptors

Similarly, receptors can be prepared from a Python script ‘prepare_receptor.py’ (or ‘prepare_receptor4.py’ for Autodock4) present in the directory mentioned above. You can also download it from here or here.

Keep your receptor files in a directory in pdb format and run this script as follows:

$ python prepare_receptor.py -r receptor.pdb -v -o receptor.pdbqt -A

Here, -r defines the receptor filename, -o is the output file, -v is for displaying processing (default is minimal output), and -A is used for checking hydrogens.

For more arguments, type $ python prepare_receptor.py -h.

References

1. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791.
2. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461.