Latest cpinutil.py and explicit solvent messages?
jchodera opened this issue · comments
I realize we're using a possibly-outdated version of cpinutil.py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.
I realize we're using a possibly-outdated version of cpinutil.py for our current tests.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).
I've actually been using the version included in AmberTools14 to generate new cpin files, which is working fine for me so far.
Yes, there should be no real difference.
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.
For now, we're using ambertools.