Merge pull request #177 from talagayev/protein_fix

Fixes individual `protein` simulation Issues

Author: talagayev

CHANGELOG.md

@@ -26,6 +26,7 @@ talagayev, NDoering99
 - Addition of `CHARM2024` forcefield (2025-11-03, PR #163)
 
 ### Fixed
+- Fixed errors during only `protein` simulation (2026-01-22, PR #177)
 - Fixed errors during postprocessing in `post_md_conversion.py` (2026-01-21, PR #176)
 - Fixed 'warinings' import error for 'openmmdlsetup.py' (2026-01-18, PR #173)
 - Adjusted the water selection for `Amber19` (2025-12-08, PR #166)

openmmdl/openmmdl_setup/openmmdlsetup.py

@@ -1078,6 +1078,9 @@ def write(self, string):
                 script.append("smallMoleculeForceField = '%s'" % session["smallMoleculeForceField"])
                 script.append("smallMoleculeForceFieldVersion = '%s'" % session["smallMoleculeForceFieldVersion"])
                 script.append("sanitization = %s" % session["ligandSanitization"])
+            elif session["sdfFile"] == "":
+                script.append("smallMoleculeForceField = None")
+                script.append("smallMoleculeForceFieldVersion = None")
             water = session["waterModel"]
     elif fileType == "amber":
         script.append("""####### Add the Amber Files in the Folder with this Script ####### \n""")

openmmdl/openmmdl_simulation/scripts/post_md_conversions.py

@@ -104,6 +104,16 @@ def _has_pbc(ts):
         dims = np.asarray(dims[:3], dtype=float)
         return np.all(np.isfinite(dims)) and np.all(dims > 0.0)
 
+    def _can_unwrap(ag):
+        """unwrap() needs fragments -> fragments needs bonds."""
+        if ag.n_atoms == 0:
+            return False
+        try:
+            _ = ag.fragments  # triggers NoDataError if no bonds
+            return True
+        except Exception:
+            return False
+
     def reimage_to_reference(mobile_ag, ref_ag):
         """
         Translate mobile_ag so its COM is minimum-image to ref_ag COM.
@@ -185,12 +195,14 @@ def _apply_pre_alignment_transforms(u):
 
         # Make protein whole, keep chains together
         if protein.n_atoms:
-            transforms.append(trans.unwrap(protein))
+            if _can_unwrap(protein):
+                transforms.append(trans.unwrap(protein))
             transforms.append(reimage_segments_to_reference(protein))
 
         # Keep ligand in same protein image
         if lig.n_atoms and protein.n_atoms:
-            transforms.append(trans.unwrap(lig))
+            if _can_unwrap(lig):
+                transforms.append(trans.unwrap(lig))
             transforms.append(reimage_to_reference(lig, protein))
 
         # Keep lipids around protein image (optional)