From 73d2daae7d4cfaf96d0f3c0e2f7e9987ee2ab780 Mon Sep 17 00:00:00 2001
From: acthiel212 <acthiel212@gmail.com>
Date: Tue, 5 May 2026 13:55:45 -0500
Subject: [PATCH] Fix to MutatePDB so patches are not discarded after mutations
 are made.

---
 .../main/java/ffx/algorithms/commands/MutatePDB.java  | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/modules/algorithms/src/main/java/ffx/algorithms/commands/MutatePDB.java b/modules/algorithms/src/main/java/ffx/algorithms/commands/MutatePDB.java
index 59f15153fe..06e5f39540 100644
--- a/modules/algorithms/src/main/java/ffx/algorithms/commands/MutatePDB.java
+++ b/modules/algorithms/src/main/java/ffx/algorithms/commands/MutatePDB.java
@@ -205,6 +205,17 @@ public MutatePDB run() {
     CompositeConfiguration properties = Keyword.loadProperties(structureFile);
     ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
     ForceField forceField = forceFieldFilter.parse();
+    String[] patches = properties.getStringArray("patch");
+    if (patches != null) {
+      for (String patch : patches) {
+        logger.info(" Attempting to read force field patch from " + patch + ".");
+        CompositeConfiguration patchConfiguration = new CompositeConfiguration();
+        patchConfiguration.addProperty("parameters", patch);
+        forceFieldFilter = new ForceFieldFilter(patchConfiguration);
+        ForceField patchForceField = forceFieldFilter.parse();
+        forceField.append(patchForceField);
+      }
+    }
     molecularAssembly.setForceField(forceField);
 
     PDBFilter pdbFilter = new PDBFilter(structureFile, molecularAssembly, forceField, properties);