Batch Submission for AutoDock Vina

This script is for use with AutoDock Vina on MacOS and Linux machines.

To use this script, prepare the ligand .pdbqt files and place them into the input folder. The receptor .pdbqt file should be placed in the main directory. The params.txt file should contain all the information inputted into a configuration file for AutoDock Vina (center_x, center_y, center_z, size_x, size_y, size_z define the Grid Box and are required). This should also be put into the main directory. Please refer to the diagram below for the file structure. AutoDock Vina is a prerequisite software needed for this script to work. As per any script, please provide execution privileges by using $ chmod +x submit.sh before trying to run the script. This is a one time step.

.
+-- batch
|  +-- input
|     +-- [ligand1].pdbqt
|     +-- [ligand2].pdbqt
|     +-- [...]
|  +-- params.txt
|  +-- [receptor].pdbqt
|  +-- submit.sh

The syntax to use the script is as follows:

$ cd ~/path/to/batch/
$ ./submit.sh input [receptor].pdbqt params.txt ~/path/to/Vina/bin/vina

_{Please note that if the Vina executable is installed in the user's bin folder, one can just use ./submit.sh input [receptor].pdbqt params.txt vina}

Please acknowledge use of this script in any publication containing results from the use of this script in the following manner: "Batch Submission Script for AutoDock Vina by Bhavesh Ashok (github.com/bhaveshashok/AutoDockVina-BatchSubmission/)". Citation of this github repository is also required.

If you choose to make modifications to this script, please acknowledge or cite this script as a foundation as outlined above.