Log in and environment set up in ARCHER
Overview
Teaching: 5 min
Exercises: 0 minQuestions
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
.