diff --git a/openff/evaluator/protocols/paprika/coordinates.py b/openff/evaluator/protocols/paprika/coordinates.py
index 0fe4afe2..8c18e706 100644
--- a/openff/evaluator/protocols/paprika/coordinates.py
+++ b/openff/evaluator/protocols/paprika/coordinates.py
@@ -171,7 +171,9 @@ def _execute(self, directory, available_resources):
         from openmm import app
         from paprika.evaluator import Setup
 
-        mdtraj_trajectory = mdtraj.load_pdb(self.complex_file_path)
+        mdtraj_trajectory = mdtraj.load_pdb(
+            self.complex_file_path, standard_names=False
+        )
 
         atom_indices_by_role = _atom_indices_by_role(
             self.substance, self.complex_file_path