Atom type specificied in XML forcefield file should be used in as the atom type in the forcefield

[GregorySchwing]

Describe the behavior you would like added to mBuild
MosDef currently provides an atom type xml section, and this section has an entry for name. The name is disregarded when writing the forcefield file, and the names of the atoms types are lettered from A ...Z. The atom type name provided by the user is only listed in a comment.

Describe the solution you'd like
Instead of naming the atom types A, B, C, D..., the user specified atom type should be used to ensure compatability with other forcefield parameter files.

An example Charmm TIP3P water XML forcefield, Mosdef script, and output forcefield file is attached.

1-2-solvate.zip

[bc118]

@GregorySchwing Yes, this makes sense for NAMD, GOMC, and the CHARMM FF. However, this is not how GROMACS and other simulation engines work. Other engines use the atom class as some common parameters like LJ constants (sigma and epsilon), and the atom type can handle the additional charges. NAMD and GOMC essentially do the same thing, handling the charges in the PSF, without explicitly calling them the atom types.

I previously discussed this with the MoSDeF team, and it makes sense to keep it the way it is based on MoSDeF being used for many other simulation engines also.