Latest cpinutil.py and explicit solvent messages?

[John Chodera]

I realize we're using a possibly-outdated version of cpinutil.py for our current tests.

@swails: Where should we get the most up-to-date version of this tool?

Also, I'm wondering what this warning means:

Warning: Carboxylate residues in explicit  solvent simulations require a modified
topology file! Use the -op flag to print one.

[Jason Swails]

I realize we're using a possibly-outdated version of cpinutil.py for our current tests.

I actually dumped it in ParmEd. The parmed/amber/titratable_residues.py has the definitions for all of the titratable residues, their charge vectors, and their reference energies. The driver script itself is in the test/ directory to ensure coverage of titratable_residues.py

Also, I'm wondering what this warning means:

Irrelevant for your uses. Explicit solvent uses GB for the proton exchanges, and to get that working I had to reduce the solvation radii for the carboxylate oxygens (which required writing a new topology file). Since you're not using GB in explicit solvent for the proton exchanges, this doesn't apply (but that also means that the reference energies also don't apply).

[Bas Rustenburg]

I've actually been using the version included in AmberTools14 to generate new cpin files, which is working fine for me so far.

[Jason Swails]

Yes, there should be no real difference.

[John Chodera]

OK. We should either expunge the old version in this repo and document that (or better yet, get cpinutil into ambermini) or pull in the latest version.

[Bas Rustenburg]

For now, we're using ambertools.