Getting PDB2PQR


Before you begin! PDB2PQR funding is dependent on your help for continued development and support. Please register before using the software so we can accurately report the number of users to our funding agencies.

Web servers

Most functionality is available through our online web servers.

The PDB2PQR web server offers a simple way to use both APBS and PDB2PQR without the need to download and install additional programs.

After registering, please visit to access the web server.

Python Package Installer (PIP)

Most users who want to use the software offline should install it via pip with the following command

pip install pdb2pqr

from within your favorite virtual environment.

The PIP package provides the pdb2pqr Python module as well as the pdb2pqr program which can be used from the command line.

Installation from source code

You can also download the source code from GitHub (we recommend using a tagged release) and building the code yourself with:

pip install .

from the top-level of the source code directory. Note that developers may want to install the code in “editable” mode with

pip install -e .


The software can be tested for correct functioning via with

coverage run -m pytest

or pytest

python -m pytest

from the top level of the source directory. These commands run basic tests; more extensive testing can be performed by adding the --run-long option to these commands.