Fixed bugs that affected nucleotides in AMOEBA

4daa1acb · Peter Eastman · fd473eea · 4daa1acb
Commit 4daa1acb authored Nov 19, 2015 by Peter Eastman
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wrappers/python/simtk/openmm/app/forcefield.py wrappers/python/simtk/openmm/app/forcefield.py +2 -2

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--- a/wrappers/python/simtk/openmm/app/forcefield.py
+++ b/wrappers/python/simtk/openmm/app/forcefield.py
@@ -2656,7 +2656,7 @@ class AmoebaPiTorsionGenerator:
            atom1 = bond.atom1
            atom2 = bond.atom2

-            if (len(data.atomBonds[atom1]) == 3 and len(data.atomBonds[atom1]) == 3):
+            if (len(data.atomBonds[atom1]) == 3 and len(data.atomBonds[atom2]) == 3):

                type1 = data.atomType[data.atoms[atom1]]
                type2 = data.atomType[data.atoms[atom2]]
@@ -2941,7 +2941,7 @@ class AmoebaTorsionTorsionGenerator:

                                # match in reverse order

-                                if (type5 in types1 and type4 in types2 and type3 in types3 and type2 in types4 and type1 in types5):
+                                elif (type5 in types1 and type4 in types2 and type3 in types3 and type2 in types4 and type1 in types5):
                                    chiralAtomIndex = self.getChiralAtomIndex(data, sys, ib, ic, id)
                                    force.addTorsionTorsion(ie, id, ic, ib, ia, chiralAtomIndex, self.gridIndex[i])