If you downloaded the tutorial from the web, the files that you will be needing can be found in a directory called topology-tutorial-files. If you received the files through a workshop, they can be found in the same directory under the path /Workshop/topology-tutorial.
cd <path to topology-tutorial-files directory>
You can list the content of this directory, by using the command ls.
This will place you in the directory containing all the necessary files. In the figure below, you can see the structure of this directory.
In this section you will learn about typical situations in which you may need to create your own topology file for a given protein or biological molecule. You will learn about biological systems which utilize amino acids other than the ``naturally occurring" 20 and how you may simply be able to alter topology file entries to account for non-standard amino acids without needing to do any new parameterization.