Merge pull request #166 from talagayev/lipid21_implementation

Fix `Amber19` Water model

Author: talagayev

CHANGELOG.md

@@ -24,6 +24,7 @@ talagayev
 - Addition of `CHARM2024` forcefield (2025-11-03, PR #163)
 
 ### Fixed
+- Adjusted the water selection for `Amber19` (2025-12-08, PR #166)
 - Fixes import error in `visualization.ipynb` (2025-10-14, PR #159)
 - Fixes numpy error in due current incompatbility with parmed (2025-10-19, PR #160)
 

openmmdl/openmmdl_simulation/scripts/forcefield_water.py

@@ -215,6 +215,8 @@ def generate_transitional_forcefield(
     if add_membrane:
         if protein_ff in old_amber:
             transitional_forcefield = app.ForceField(protein_ff, "tip3p.xml", "amber14/lipid17.xml")
+        elif protein_ff == "amber19-all.xml":
+            transitional_forcefield = app.ForceField(protein_ff, "amber19/tip3p.xml",)
         else:
             transitional_forcefield = app.ForceField(protein_ff, "amber14/tip3p.xml")
     else:

openmmdl/tests/openmmdl_simulation/forcefield_water_test.py

@@ -336,3 +336,9 @@ def test_generate_transitional_forcefield(sample_rdkit_molecule):
         "amber14-all.xml", "tip3p.xml", True
     )
     assert isinstance(transitional_forcefield_4, app.ForceField)
+
+    # Test for amber19
+    transitional_forcefield_5 = generate_transitional_forcefield(
+        "amber19-all.xml", "amber19/tip3p.xml", False, "gaff", sample_rdkit_molecule
+    )
+    assert isinstance(transitional_forcefield_5, app.ForceField)