Upload refine.py

scripts/refine.py

@@ -35,7 +35,8 @@ def polish_design(target_pdb_id, uploaded_file_path):
     modeller.addHydrogens(forcefield)
     
     # Setup the system using the REPAIRED modeller topology
-    system = forcefield.createSystem(modeller.topology)
+    # Note: ignoreExternalBonds=True kills the LYS 155 error
+    system = forcefield.createSystem(modeller.topology, ignoreExternalBonds=True)
     integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picosecond)
     simulation = Simulation(modeller.topology, system, integrator)
     simulation.context.setPositions(modeller.positions)