[enchancement] always write out a PDB of the system that has all atoms present

[IAlibay]

There are quite a few occasions where having a copy of the system with all the atoms can be helpful (debugging, etc..). Since it's a single file we should try to write it out all the time.

[IAlibay]

This might be good to do ahead of alchemistry since it's a nice QoL thing folks tend to need.