--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 23:33:40	432
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/28 19:33:37	435
@@ -783,8 +783,8 @@ void SimSetup::makeMolecules( void ){
       theBonds[j].a = currentBond->getA() + atomOffset;
       theBonds[j].b = currentBond->getB() + atomOffset;
 
-      exI = theBonds[i].a;
-      exJ = theBonds[i].b;
+      exI = theBonds[j].a;
+      exJ = theBonds[j].b;
 
       // exclude_I must always be the smaller of the pair
       if( exI > exJ ){
@@ -800,6 +800,7 @@ void SimSetup::makeMolecules( void ){
       
       the_excludes[j+excludeOffset]->setPair( exI, exJ );
 #else  // isn't MPI
+
       the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
 #endif  //is_mpi
     }
@@ -837,7 +838,7 @@ void SimSetup::makeMolecules( void ){
 	      
 	    default:
 	      sprintf( painCave.errMsg,
-		       "SimSetup Error: ghostVectorSource was neiter a "
+		       "SimSetup Error: ghostVectorSource was neither a "
 		       "double nor an int.\n"
 		       "-->Bend[%d] in %s\n",
 		       j, comp_stamps[stampID]->getID() );
@@ -937,9 +938,15 @@ void SimSetup::makeMolecules( void ){
     delete[] theTorsions;
   }
 
+#ifdef IS_MPI
+  sprintf( checkPointMsg, "all molecules initialized succesfully" );
+  MPIcheckPoint();
+#endif // is_mpi
+
   // clean up the forcefield
   the_ff->calcRcut();
   the_ff->cleanMe();
+
 }
 
 void SimSetup::initFromBass( void ){