How to Start Cassandra

Thank you so much for your helping. I spent couple last days for learning Cassandra. I started with the most basic example which is Methane. However, I have a problem when I ran it. I hope you can help

First, when I run the CH4.pdb file to create the CH4.ff file. As on the photo, I can only enter LJ but not for the value. I have to open the CH4.ff file to manually enter the value. I am not sure if it is the way to enter or my Ubuntu has problem. Please confirm.

Second, the CH4.ff is created on the home folder, not in the direction of CH4.pdb file. I have to copy and the .ff file to .pdb file to be the same location.

Third, even I have the CH4.ff and CH4.pdb in the same folder, but I couldn't run the python code to create methane.mcf file. Also, I tried the original file on example but it can't still run. I attach two photos for details.
I appreciate so much for your help.