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Commit 12ff40ef authored by Peter Eastman's avatar Peter Eastman
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Bonds were being added to the Topology incorrectly

parent a4673043
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wrappers/python/simtk/openmm/app/amberprmtopfile.py
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...@@ -99,10 +99,11 @@ class AmberPrmtopFile(object): ...@@ -99,10 +99,11 @@ class AmberPrmtopFile(object):
# Add bonds to the topology # Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH(): for bond in prmtop.getBondsWithH():
top.addBond(bond[0], bond[1]) top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH(): for bond in prmtop.getBondsNoH():
top.addBond(bond[0], bond[1]) top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size. # Set the periodic box size.
......
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