pdb2pqr command not found

In this troubleshooting guide we learn how to fix pdb2pqr command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

pdb2pqr: command not found

or when using sudo you get the following error message

sudo: pdb2pqr: command not found

Solutions to pdb2pqr: command not found

How To Fix pdb2pqr: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu pdb2pqr is provided by pdb2pqr package.

pdb2pqr is:

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides 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

This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.

To fix this problem, we can install more using the command below.

sudo apt-get -y install pdb2pqr

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install pdb2pqr.

sudo apt -y install pdb2pqr

Or if you have aptitude installed you can use the following command.

sudo aptitude install pdb2pqr

Summary

In this tutorial we learn how to fix pdb2pqr command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.