Added prmtop to openmm tutorial

[jaketanderson]

Running the openmm tutorial currently creates errors during the analysis phase due to the absence of a prmtop file attribute of the analysis.fe_calc() object free_energy. Since cb6-but-dum.prmtop is already easily accessible in each window, this PR serves as a quick fix to avoid errors along the lines of could not initialize prmtop topology directly and/or 0-atom structure.

I haven't gotten the chance to try running the gromacs or namd tutorials, but if a similar issue is found in those notebooks defining the prmtop attribute might also be a fix for them.

Questions:

• Is a prmtop file really necessary here? Is it required because some part of the analysis pipeline assumes that the simulation was run with AMBER? If that's the case, this won't fix the underlying issue, just add a bandage
• Is this error also created when running the tutorials for gromacs and namd? I haven't checked yet but I hypothesize the error will occur in all non-AMBER tutorials

[codecov-commenter]

Codecov Report

Merging #173 (d4a8c03) into master (5376f44) will not change coverage. The diff coverage is n/a.

[jeff231li]

@jaketanderson I think this is a version issue. I suspect you have pAPRika version 1.1.0 installed and the jupyter notebook you're using is probably from the master branch of the repository. The master branch includes a new variable fe_calc.topology, which supersedes fe_calc.prmtop. The OpenMM tutorial on the stable version of the docs uses prmtop https://paprika.readthedocs.io/en/stable/tutorials/04-tutorial-cb6-but-openmm.html.

[jaketanderson]

@jaketanderson I think this is a version issue. I suspect you have pAPRika version 1.1.0 installed and the jupyter notebook you're using is probably from the master branch of the repository. The master branch includes a new variable fe_calc.topology, which supersedes fe_calc.prmtop. The OpenMM tutorial on the stable version of the docs uses prmtop https://paprika.readthedocs.io/en/stable/tutorials/04-tutorial-cb6-but-openmm.html.

You're totally right Jeff, I was using the latest from master but mistakenly using my older conda environment. Thank you for taking time to check this out :)

Closing the PR.

[slochower]

Time to cut a new release?