How To Install mgltools-cadd on Ubuntu 18.04
Introduction
In this tutorial we learn how to install mgltools-cadd on Ubuntu 18.04.
What is mgltools-cadd
mgltools-cadd is:
This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds.
The Computer Aided Drug Discovery (CADD) Pipeline is a workflow environment designed to support molecular dyanmics simulations and virtual screening experiments for in silico drug discovery, with a special focus on supporting the use of the Relaxed Complex Scheme. It includes web based access to applications such as NAMD, AutoDock, PDB2PQR, APBS, MGLToos and couples them in a flexible and scalable fashion through cloud computing. It is developed as a standalone application, using Vision (https://www.nbcr.net/pub/wiki/index.php?title=MGLTools#Vision) as the backend engine for visual programming and workflow execution. The scientific applications are made accessible through CADD using Opal Web services (https://www.nbcr.net/pub/wiki/index.php?title=Opal) for scalable and distributed computation.
The workflow components of the CADD pipeline are currently released as Vision networks packaged for specific processes in a modular fashion. These modules may be coupled at ease for more complex processes. In the future, they may also be accessible from workflow repositories such as MyExperiment.org, and from AutoDockTools. The Opal services used in the CADD workflow may be accessed using programmatic access, the Opal Server Dashboard or other workflow clients such as Kepler, VisTrails or Taverna through Opal plugins available at Opal Sourceforge website (http://opal.nbcr.net).
Features
- Automatic launching of NAMD simulation on TeraGrid and NBCR resources, including experimental support for migration of simulation between resources.
- Selection of representative snapshots/conformations from MD simulations using clustering tools such as QR factorization from VMD and Ptraj from Amber.
- Support of Virtual Screening using AutoDock, AutoDock Vina
- Support of Relaxed Complex Scheme based Virtual Screening and Rescoring
- Visualization and analysis of Virtual Screening hits
There are three methods to install mgltools-cadd on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install mgltools-cadd Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install mgltools-cadd using apt-get by running the following command:
sudo apt-get -y install mgltools-cadd
Install mgltools-cadd Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install mgltools-cadd using apt by running the following command:
sudo apt -y install mgltools-cadd
Install mgltools-cadd 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 mgltools-cadd using aptitude by running the following command:
sudo aptitude -y install mgltools-cadd
How To Uninstall mgltools-cadd on Ubuntu 18.04
To uninstall only the mgltools-cadd package we can use the following command:
sudo apt-get remove mgltools-cadd
Uninstall mgltools-cadd And Its Dependencies
To uninstall mgltools-cadd and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove mgltools-cadd
Remove mgltools-cadd Configurations and Data
To remove mgltools-cadd configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge mgltools-cadd
Remove mgltools-cadd configuration, data, and all of its dependencies
We can use the following command to remove mgltools-cadd configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge mgltools-cadd
References
Summary
In this tutorial we learn how to install mgltools-cadd package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
