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):