From ddef28f52599d6f4152ad36c77d7b19a84240ba7 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Wed, 13 Mar 2024 16:06:47 +0000
Subject: [PATCH] Exclude ions from the perturbation.

---
 src/somd2/runner/_somd1.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/somd2/runner/_somd1.py b/src/somd2/runner/_somd1.py
index 407a831..19ba9eb 100644
--- a/src/somd2/runner/_somd1.py
+++ b/src/somd2/runner/_somd1.py
@@ -648,12 +648,14 @@ def _apply_pert(system, pert_file):
     # Try to apply the perturbation to each non-water molecule.
     is_pert = False
     for mol in non_waters:
-        try:
-            pert_mol = _morph.create_from_pertfile(mol, pert_file)
-            is_pert = True
-            break
-        except:
-            pass
+        # Exclude ions.
+        if mol.num_atoms() > 1:
+            try:
+                pert_mol = _morph.create_from_pertfile(mol, pert_file)
+                is_pert = True
+                break
+            except:
+                pass
 
     if not is_pert:
         raise ValueError(f"Failed to apply the perturbation in '{pert_file}'.")