ligand_pdb2pdbqt

Automated Windows pipeline that protonates ligand PDB files at pH 7.4 and converts them in bulk to AutoDock-ready PDBQT format using Open Babel 3 + MGLTools

Ligand(PDB)-to-PDBQT Preparation Pipeline

Automated ligand cleanup & conversion for AutoDock Vina

Overview

This repository contains a Windows-centric batch script (prepare_all_pdb_v2.bat) that:

1. Checks you have Open Babel ≥ 3.1.1 and MGLTools 1.5.7 installed.
2. Batch-protonates every .pdb file found in .\lib\ at physiological pH 7.4.
3. Converts the protonated models to AutoDock-compatible .pdbqt format via prepare_ligand4.py.
4. Drops final files into .\pdbqt-2\.
5. Cleans up all temporary scratch files.

Why? Preparing hundreds of ligands manually is error-prone.
This script standardises protonation and file naming so downstream AutoDock Vina runs are reproducible.

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Quick start

git clone https://github.com/SidSin0809/ligand_pdb2pdbqt.git

:: Place all ligand PDB files in .\lib\
prepare_all_pdb_v2.bat


| Dependency               | Version tested          | Install hint                                |
| ------------------------ | ----------------------- | ------------------------------------------- |
| Open Babel               | 3.1.1                   | [https://openbabel.org/]
| MGLTools (AutoDockTools) | 1.5.7                   | [https://ccsb.scripps.edu/mgltools/]
| Python                   | 3.9 (MGLTools-embedded) | Bundled inside MGLTools
| Windows                  | 10/11                   | Uses `cmd`-style batch syntax

Citation If you use this pipeline in academic work, please cite: O’Boyle et al. “Open Babel: An open chemical toolbox” J Cheminform 2011. Morris GM et al. “AutoDockTools4: Automated docking tools” J Comput Chem 2009.