Environment set up and downloading files

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• Which software will be used in this workshop?

Objectives

• Download necessary data for the workshop

In this session we are going to use several software packages:

• AmberTools (We will use the latest version of Ambertools. If you are using an older version, commands might run slightly different.)
• PROPKA or PROPKA server
• OpenBabel
• Pymol or VMD or another molecular visualisation tool of your preference.
• Marvin Sketch.

You should check that both pymoland babelare installed in your workstation. Try to type pymol anb babel respectively. If they are not installed you should download them using the following command:

apt-get install pymol
apt-get install babel

If you have any trouble, let us know.

Downloading data

You’ll need to download some files to follow this workshop, since there is no git installed. You should visit this page and download the files.

About the data

It provides:

• PDB file with the initial coordinates. For this workshop we will use a X-ray structure of the main protease of the SARS-CoV2 virus (PDB id 5R84) with a small-molecule bound to its catalytic site.
• AmberTools input files (LEap, sander and cpptraj input files)
• Topology, coordinates and trajectory files.

Once you have downloaded the files you can go into the files_MDbasictutorial folder and proceed to the next section:

cd files_MDbasictutorial

Key Points

• We need several pieces of software to model biological systems