Lester Hedges

No, there's nothing in BioSImSpace to create groups or index files. If you're using existing GROMACS groups then I'd suggest just writing your own wrapper to `gmx make_ndx` in `a3fe`,...

No, we only call `grompp` with options required for the existing protocols, you'd need to wrap a different call to it within `a3fe`. In the non sandpit code there is...

All builds appear to fail during the wrapper compilation, albeit at different points. For Linux, the error is: ``` In file included from /home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/pkgs/sire-2025.1.0/include/Sire/SireError/errors.h:31, from /home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/work/wrapper/python/main.cpp:14: /home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/pkgs/sire-2025.1.0/include/Sire/sireglobal.h:91:10: fatal error: boost/current_function.hpp:...

Other than the CI issues, this is working nicely. I've tested via BioSimSpace and can parameterise using ff19SB just fine.

Ooof, that's annoying. It's not even that we could load the most recent template from the `ambertools` dat directory, then use Sire to rename the residues, since the charge is...

I guess that wouldn't matter if you're reparametrising anyway, so maybe we could just swap the template. The fiddly bit would be working out what template was included. We could...

We are currently experiencing strange failures for _all_ Windows CI of Sire, which means that Windows conda builds for BioSimSpace are currently unavailable. See [here](https://github.com/OpenBioSim/sire/issues/268) for details.