Raise helpful error message when reactive smarts doesn't match

[diogomart]

Currently we get the following, which is does not help the user figure out the problem. Thanks @althea-hansel for finding this one

meeko/preparation.py", line 577, in prepare

    self.deprecated_setup_access = setups[0]

IndexError: list index out of range

[rwxayheee]

This was addressed by 82c5702