How To Install pdb2pqr on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 449 words
Introduction
In this tutorial we learn how to install pdb2pqr on Ubuntu.
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. 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
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, 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 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
Dependencies
pdb2pqr have the following dependencies:
References
Summary
In this tutorial we learn how to install pdb2pqr package on Ubuntu using different package management tools: apt, apt-get and aptitude.