Log in and environment set up in ARCHER

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How do I access ARCHER?

• How do I set up the correct environment in ARCHER?

Objectives

• Log in to ARCHER.

• Load AmberTools module in ARCHER.

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.)
• CP2K
• PROPKA or PROPKA server
• OpenBabel
• Pymol or VMD or another molecular visualisation tool of your preference.
• Marvin Sketch.

We are going to use AmberTools and CP2K on ARCHER.

Log in to ARCHER:

For your convenience, all the required software has been installed in ARCHER. Therefore, you have to log in with the credential that have been sent to you.

ssh -XY user@login.archer.ac.uk

Load the environment

First, to set up the proper environment you should run the following commands on ARCHER. These set of commands will give you access to the installed software:

module swap PrgEnv-cray PrgEnv-gnu
module load amber-tools/20 
module load propka
module load openbabel/2.4.1

Then we should move to out work folder. You should substitute XXX for the project name and YYY for your username:

pwd
cd /work/XXX/XXX/YYY/

Downloading data

Next, you need to download some files to follow this workshop:

git config --global http.sslverify false
git clone https://git.ecdf.ed.ac.uk/sllabres/files_ambertools4cp2k.git

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.
• ARCHER submission scripts.
• AmberTools input files (LEap, sander and cpptraj input files)
• CP2K input file.

Once you have downloaded the files you can go into the files_ambertools4cp2k folder and proceed to the next section:

cd files_ambertools4cp2k

Key Points

• SSH to ARCHER

• Load Ambertools with module load.