Use untyped system to remove H

- foyer.Forcefield.apply does not carry over the set atomic_number info
from the pmd_structure. mosdef-hub/foyer/issues/466 This workaround will
fix it.

planckton/init.py

@@ -181,9 +181,7 @@ def pack(self, box_expand_factor=5):
         pmd_system = system.to_parmed(residues=[self.residues])
         typed_system = self.ff.apply(pmd_system, **self.foyer_kwargs)
         if self.remove_hydrogen_atoms:
-            typed_system.strip(
-                [a.atomic_number == 1 for a in typed_system.atoms]
-            )
+            typed_system.strip([a.atomic_number == 1 for a in pmd_system.atoms])
         return typed_system
 
     def _calculate_L(self):