- Return to the main setup page
- Python tutorial setup page
- Homology modelling tutorial setup page
- Docking tutorial setup page
Included here are instructions to help you get started with the Oxford Computational Biochemistry MD course.
The instructions are split into two parts:
- Setup
These instructions should be followed prior to attending the tutorial. This will walk you through; installing the necessary software, obtaining your ARCUS account, and testing that everything works as expected.
- Starting the tutorial
These instructions should be followed on the day of / when starting the tutorial. We assume here that you have completed the setup instructions on the same machine and that testing passed as expected.
This tutorial uses the same conda environment as the one used in the Python
tutorial. You will therefore have to complete the Python tutorial setup instructions
beforehand.
Using a terminal browse (i.e. using cd) to your local installation of this tutorial.
Then we want to activate the conda environment:
conda activate OxPython
If this fails, it may be that the Python tutorial setup was unsuccessful.
The remainder of the setup instructions are in the 00_Setup.ipynb notebook.
Start jupyter notebook:
jupyter notebook
And click on 00_setup.ipynb in your browser to open the instructions.
Once finished with the notebook, please remember to deactivate your conda environment:
conda deactivate
You can now continue with the setup for the other tutorials. See "Navigation" above for links to the other setup instructions.
Assuming you have already completed the setup instructions, open a terminal and navigate to the MD tutorial.
Then activate the conda environment:
conda activate OxPython
And start the tutorial by typing:
jupyter notebook
You should then make your way through the notebooks starting with 01_Introduction.ipynb.
Please note that you will also be required to also have an opened terminal (linux/macOS) or MobaXterm instance (Windows) in order to connect to ARCUS.