I am trying to perform docking using Autodock4, and I have a specific task in mind. I've downloaded a ligand library, and I need a script that will automatically dock each ligand from this library sequentially. With Autodock Vina, this is possible, and the relevant script is provided below:
#! /bin/bash
for f in ligand_*.pdbqt; do
b=`basename $f .pdbqt`
echo Processing ligand $b
mkdir -p $b
vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
done
However, given the numerous parameters in Autodock4 and the multiple file extensions generated during the docking process, I've found it challenging to write a similar script for Autodock4. Is it possible to automate the docking process I described using Autodock4? Any assistance would be greatly appreciated. Thank you!
I expected to be able to sequentially dock each ligand from the library without manual intervention. Is it possible for me to perform this process with Autodock4 by preparing the protein appropriately and using a similar script? Because when we do a regular docking with parameters like grid and docking, it generates specific files for the protein and ligand. Is there an alternative method?