Getting Structures Ready

Below is a quick-start guide for getting structures ready for APBS with two ways of using PDB2PQR. PDB2PQR is an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. This is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.

These tasks include:

  • Adding a limited number of missing heavy atoms to biomolecular structures
  • Determining side-chain pKas
  • Placing missing hydrogens
  • Optimizing the protein for favorable hydrogen bonding
  • Assigning charge and radius parameters from a variety of force fields

PDB2PQR Basic workflow

The first method demonstrates how to use the PDB2PQR web server and the next method calls PDB2PQR directly from the command line. For a more detailed explanation of how PDB2PQR runs, see Basic Usage.

Before you begin!

PDB2PQR funding is dependent on your support for continued development and support. Please register before using the PDB2PQR web server so we can accurately report the number of users to our funding agencies.

Web Server:

  1. Go to web server

  2. Identify your molecule:

    • Enter the protein data bank ID or…
    • Load the protein data bank file (examples here)

  • Press submit!

For more information on how to prepare files, click here

Command Line:

Running PDB2PQR with the same options shown above can be performed with the following command:

% pdb2pqr.py --ff=parse --apbs-input --ph-calc-method=propka 1FAS 1FAS.pqr

Notes on PDB2PQR

  • PDB2PQR was ported to Python by Todd Dolinsky while working with Nathan Baker at Washington University in St. Louis. The PDB2PQR code is based on C++ design and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to facilitate structure preparation for APBS.
  • PDB2PQR uses PROPKA to determine protein pKa values. PROPKA is developed by the Jensen Research Group at the University of Copenhagen. More information about PROPKA can be found at https://github.com/jensengroup/propka-3.1.
  • PEOE_PB charges for ligand parameterization were developed by Paul Czodrowski in the Klebe Group at the Philipps University Marburg.