From 3aa0cbaf9d942a6d373fd4dba99a1618b770dda9 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Tue, 2 Dec 2025 16:33:50 +0000
Subject: [PATCH] Remove AmberParams properties prior to extracting end states.

---
 src/somd2/_utils/_somd1.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/somd2/_utils/_somd1.py b/src/somd2/_utils/_somd1.py
index 44ae8d5..760bb75 100644
--- a/src/somd2/_utils/_somd1.py
+++ b/src/somd2/_utils/_somd1.py
@@ -660,6 +660,15 @@ def reconstruct_system(system):
     # Loop over all perturbable molecules.
     for mol in pert_mols:
 
+        # Delete an AmberParams properties.
+        try:
+            cursor = mol.cursor()
+            del cursor["parameters0"]
+            del cursor["parameters1"]
+            mol = cursor.commit()
+        except:
+            pass
+
         # Extract the end states.
         ref = _morph.extract_reference(mol)
         pert = _morph.extract_perturbed(mol)