Protein-ligand complex tutorial errors

The tutorial uses a slightly older version of the CHARMM36 port that did not have a certain terminal patch that screws up methionine. You need to interactively select the NH3+ terminus type with -ter added to the pdb2gmx command.

You should not have to make any changes to force field files.

This is unnecessary. The tutorial should work cleanly without any real extra effort with outside programs. I will probably update it soon for those users who are using the July 2022 CHARMM36 port. The tutorial uses one from March 2019 (which is still available online, so the tutorial can be completed as written).