How To Install pdb2pqr on Ubuntu 22.04

In this tutorial we learn how to install pdb2pqr on Ubuntu 22.04. pdb2pqr is Preparation of protein structures for electrostatics calculations

Introduction

In this tutorial we learn how to install pdb2pqr on Ubuntu 22.04.

What is pdb2pqr

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.

There are three methods to install pdb2pqr on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install pdb2pqr Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pdb2pqr using apt-get by running the following command:

sudo apt-get -y install pdb2pqr

Install pdb2pqr Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pdb2pqr using apt by running the following command:

sudo apt -y install pdb2pqr

Install pdb2pqr Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install pdb2pqr using aptitude by running the following command:

sudo aptitude -y install pdb2pqr

How To Uninstall pdb2pqr on Ubuntu 22.04

To uninstall only the pdb2pqr package we can use the following command:

sudo apt-get remove pdb2pqr

Uninstall pdb2pqr And Its Dependencies

To uninstall pdb2pqr and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove pdb2pqr

Remove pdb2pqr Configurations and Data

To remove pdb2pqr configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge pdb2pqr

Remove pdb2pqr configuration, data, and all of its dependencies

We can use the following command to remove pdb2pqr configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pdb2pqr

References

Summary

In this tutorial we learn how to install pdb2pqr package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.