Fix bug resulting from mdtraj/mdtraj#1611

Author: SimonBoothroyd

openff/evaluator/protocols/coordinates.py

@@ -244,6 +244,10 @@ def _save_results(self, directory, trajectory):
             The trajectory of the created system.
         """
 
+        # Fix mdtraj #1611
+        for atom in trajectory.topology.atoms:
+            atom.serial = None
+
         self.coordinate_file_path = path.join(directory, "output.pdb")
         trajectory.save_pdb(self.coordinate_file_path)
 

openff/evaluator/utils/packmol.py

@@ -681,6 +681,10 @@ def pack_box(
 
         trajectory = mdtraj.load_pdb(structure_to_solvate)
 
+        # Fix mdtraj #1611
+        for atom in trajectory.topology.atoms:
+            atom.serial = None
+
         structure_to_solvate = "solvate.pdb"
         trajectory.save_pdb(os.path.join(working_directory, structure_to_solvate))