Setting up Open Babel for Ligand library preparation

Open Babel is used for managing the ligand libraries for virtual screening and protein docking. Ligand libraries are mostly available as SDF files which have to be converted to Autodock Vina compatible PDBQT format. This can be done easily using the Open Babel GUI. Open Babel installation is explained in this post.

Windows build is available at this site. However since most of the analysis is best done on a Linux computer, we will be compiling and installing the latest version from their website. Even though Open Babel is available from software repositories, we need version 2.4 and above. For those using AUR (Arch, Manjaro, Antergos, etc), you may simply find and install it from your package manager. Those on Ubuntu and derivatives, may follow the instructions here.

Open Babel Installation

Start by downloading the source code for OpenBabel

Installing dependencies

C++ compiler:

sudo apt-get install build-essential

sudo apt install cmake

wxWidgets 2.8 (or newer)
sudo apt install wx3.0-headers

Optional packages that should be intalled
sudo apt-get install libxml2-dev zlib1g-dev libeigen3-dev libcairo2-dev

Building and installing

First of all, extract the tar.gz file downloaded from open babel website. cd in to the extracted folder and execute the following commands.

mkdir build
cd build
cmake ..
make -j4 (for 4 thread system)
sudo make install
cmake .. -DBUILD_GUI=ON
sudo apt install openbabel-gui

The open Babel GUI may be accessed by the command: obgui