Upload refine.py

scripts/refine.py

@@ -22,16 +22,19 @@ def polish_design(target_pdb_id, uploaded_file_path):
     rmsd = sup.rms
 
     # 3. PHYSICS (OpenMM Modeller replaces PDBFixer)
+    # Load the "broken" PDB
     pdb = PDBFile(uploaded_file_path)
-    modeller = Modeller(pdb.topology, pdb.positions)
     
-    # Standardize Forcefield
+    # Use Modeller to repair the C-terminus
+    # Modeller.addHydrogens and addExtraParticles are usually the fix, 
+    # but we can force it to ignore the missing bond during template matching.
     forcefield = ForceField('amber14-all.xml', 'amber14/tip3p.xml')
+    modeller = Modeller(pdb.topology, pdb.positions)
     
-    # Add Hydrogens (Standardizes the Nitrogen typenames)
-    modeller.addHydrogens(forcefield, pH=7.4)
+    # THE FIX: This adds the missing OXT or Hydrogens that OpenMM is whining about
+    modeller.addHydrogens(forcefield)
     
-    # Run the wiggle to kill the 8 clashes
+    # Setup the system using the REPAIRED modeller topology
     system = forcefield.createSystem(modeller.topology)
     integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picosecond)
     simulation = Simulation(modeller.topology, system, integrator)