To batch ligand PDBQT input files to AutoDock 4, you can utilize a scripting or programming language to automate the process. Here's a general approach:

import os # Specify the directory containing the ligand PDBQT files ligand_directory = "path/to/ligand/files" # Get a list of all ligand files in the directory ligand_files = os.listdir(ligand_directory) # Loop through each ligand file and run AutoDock for each for ligand_file in ligand_files: # Generate the command to run AutoDock for the current ligand file command = f"autodock4 -p receptor.pdbqt -l {os.path.join(ligand_directory, ligand_file)} -o {ligand_file}.dlg" # Run the AutoDock command os.system(command)

Make sure to replace "path/to/ligand/files" with the actual directory path where your ligand PDBQT files are located. Also, adjust the AutoDock command (autodock4) according to your specific requirements, including specifying the receptor file (receptor.pdbqt), output file name ({ligand_file}.dlg), and any other options you need.

python batch_autodock.py

The script will loop through each ligand PDBQT file in the specified directory, run AutoDock for each ligand using the receptor file, and generate the corresponding output files.

Note: Make sure AutoDock 4 is properly installed and accessible in your system's PATH for the script to execute the AutoDock command successfully.

This approach allows you to batch process multiple ligand PDBQT files with AutoDock 4, saving you time and effort compared to running the commands individually.

Also check: Article InstaDock: A single-click graphical user interface for molec...

If you just want to group the files into a single .pdbqt just

cat *.pdbqt > group.pdbqt