Merge pull request #1555 from peastman/gbbugs

Fixed bugs related to CustomGBForce

platforms/cpu/src/CpuKernels.cpp

@@ -1033,7 +1033,7 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
     nonbondedMethod = CalcCustomGBForceKernel::NonbondedMethod(force.getNonbondedMethod());
     nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
     if (nonbondedMethod != NoCutoff)
-        data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
+        data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, force.getNumExclusions() > 0, exclusions);
 
     // Create custom functions for the tabulated functions.
 

platforms/cpu/src/CpuPlatform.cpp

@@ -171,4 +171,6 @@ void CpuPlatform::PlatformData::requestNeighborList(double cutoffDistance, doubl
             anyExclusions = true;
         }
     }
+    else if (!anyExclusions)
+        exclusions = exclusionList;
 }

wrappers/python/simtk/openmm/app/internal/customgbforces.py

@@ -267,7 +267,7 @@ def _mbondi_radii(topology):
             bondeds = all_bonds[atom]
             if bondeds[0].element in (E.carbon, E.nitrogen):
                 radii[i] = 1.3
-            elif bondeds[0].type.atomic_number in (E.oxygen, E.sulfur):
+            elif bondeds[0].element in (E.oxygen, E.sulfur):
                 radii[i] = 0.8
             else:
                 radii[i] = 1.2