Bonds were being added to the Topology incorrectly

12ff40ef · Peter Eastman · a4673043 · 12ff40ef
Commit 12ff40ef authored May 07, 2012 by Peter Eastman
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wrappers/python/simtk/openmm/app/amberprmtopfile.py wrappers/python/simtk/openmm/app/amberprmtopfile.py +3 -2

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--- a/wrappers/python/simtk/openmm/app/amberprmtopfile.py
+++ b/wrappers/python/simtk/openmm/app/amberprmtopfile.py
@@ -99,10 +99,11 @@ class AmberPrmtopFile(object):
        
        # Add bonds to the topology
        
+        atoms = list(top.atoms())
        for bond in prmtop.getBondsWithH():
-            top.addBond(bond[0], bond[1])
+            top.addBond(atoms[bond[0]], atoms[bond[1]])
        for bond in prmtop.getBondsNoH():
-            top.addBond(bond[0], bond[1])
+            top.addBond(atoms[bond[0]], atoms[bond[1]])
        
        # Set the periodic box size.