GAFF/GAFF2 for foyer

[mrshirts]

Is your feature request related to a problem? Please describe.
People would like to be able to parameterize ligands with GAFF/GAFF2

Describe the solution you'd like
If we have a foyer xml file that encodes GAFF with SMILES strings, it would be really nice.

Describe alternatives you've considered
The alternatives are needing to call ambertools, and we don't want dependencies there.

Additional context
Making sure everything is encoded correctly will be challenging; this is something that there was a lot of challenges with porting ff14sb to SMIRNOFF formatting.

[mrshirts]

See https://github.com/mosdef-hub/foyer/tree/main/foyer/forcefields/xml as examples of existing files.

[joelaforet]

Where would this code live in the MuPT repository? What functions in MuPT currently call ambertools and need to be re-worked to instead pull from this XML when it is generated?

[mrshirts]

It would live in foyer https://github.com/mosdef-hub/foyer/tree/main/foyer/forcefields/xml as an xml file, i.e. like https://github.com/mosdef-hub/foyer/blob/main/foyer/forcefields/xml/oplsaa.xml

[chrisjonesBSU]

https://github.com/rsdefever/GAFF-foyer and xml files here

and in the GMSO xml format.

https://github.com/mosdef-hub/gmso/blob/main/gmso/utils/files/gmso_xmls/test_ffstyles/gaff.xml

[joelaforet]

It would live in foyer

So this would be an external contribution to the foyer repository, not MuPT?

[mrshirts]

So, it exists already? what does "test_ffstyles" mean? Is it in beta, some chemical functionality is missing, it needs to be tested?

[joelaforet]

I was also asking where in the MuPT codebase we would be interacting with this file. What functions in MuPT call Ambertools? @janitha-mahanthe Could you comment?

[chrisjonesBSU]

the gaff xml file originates from ryan defever's implementation (gaff-foyer) and has never been set up with the same testing/validation that the oplsaa.xml file does in foyer, so it's technically not officially tested. In GMSO, the test_ff_styles are xml files used for unit tests.

So far (whether this initial intention or not, I'm not sure) neither foyer nor gmso has acted as a repository for different forcefields. It's mostly been a thing where you bring your own XML file/forcefield except for OPLS-AA and a trappe-ua.

[mrshirts]

Nothing in MuPT currently calls it, but Salman was discussing using AmberTools in PolymerizeIt.

[mrshirts]

Interesting!

has never been set up with the same testing/validation that the oplsaa.xml file does in foyer

What testing/validation was done for that?

It's mostly been a thing where you bring your own XML file/forcefield except for OPLS-AA and a trappe-ua.

though practically, having somebody do it once-and-for all for often-used FF's like GAFF would be extremely useful.