From ccd4489a6208405c000fc4c8d2f494214276f3d8 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 3 Oct 2024 10:15:53 +0100
Subject: [PATCH] Update the system with the correct molecule.

---
 src/somd2/_utils/_somd1.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/somd2/_utils/_somd1.py b/src/somd2/_utils/_somd1.py
index b5772ee..056b53e 100644
--- a/src/somd2/_utils/_somd1.py
+++ b/src/somd2/_utils/_somd1.py
@@ -595,6 +595,6 @@ def _apply_pert(system, pert_file):
         raise ValueError(f"Failed to apply the perturbation in '{pert_file}'.")
 
     # Update the molecule.
-    system.update(mol)
+    system.update(pert_mol)
 
     return system