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CHARMM and AMBER forcefields for OpenMM (with small molecule support)

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* Attempts to ensure the OpenFF Toolkit is updated to the RC builds * Attempts to fix tests relying on the toolkit (see https://github.com/openmm/openmmforcefields/pull/191#issuecomment-1209131880)

This PR attempts to fix #118 and whatever broke to cause the issues reported there. - [x] Test Amber solvents conversion in nightly CI runs - [ ] Fix residue...

Adds a small warning for developers to the README; I got bit by this today.

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.1.0 to 3.1.0. Release notes Sourced from codecov/codecov-action's releases. v3.1.0 3.1.0 Features #699 Incorporate xcode arguments for the Codecov uploader Dependencies #694 build(deps-dev): bump @​vercel/ncc from 0.33.3...

dependencies

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.0.2. Release notes Sourced from actions/checkout's releases. v3.0.2 What's Changed Add set-safe-directory input to allow customers to take control. by @​TingluoHuang in actions/checkout#770 Prepare changelog...

dependencies

cc: https://github.com/openmm/openmm/issues/3678 There is a use case for adding an optional `allow_nonintegral_charges` argument that could be passed to `ForceField.create_openmm_system` in the OpenFF toolkit to permit users with manually-provided non-integral charges...

bug

Hi, Recently I noticed a few parameters relating to OP that seem to be missing from phosaa14SB.xml. These are the parameters from parm10.dat that I think might be missing from...

bug

At the moment, SmallMoleculeTemplateGenerator does not implement any file locking for the small molecule cache database. This means that the cache file can become corrupted if several processes try to...

bug

Originally identified in #164 but I didn't realize what the problem was at the time. This didn't occur in openmm7.4.2 but does in the current available version of openmm7.5. I...

bug
high-priority