Create RBFE simulation run script

[IAlibay]

We need to create a script that does the following:

• Takes a set of inputs (ligand SDFs, cofactors SDF, protein PDB)
• Create a LOMAP LigandNetwork (note needs fixing to deal with charge changes)
• Create an RBFE AlchemicalNetwork
• Selectively apply a different set of Protocol settings when dealing with net charge changes

[IAlibay]

Irfan owes residue name setting check for this.