--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/26 21:50:33	412
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/26 22:02:36	414
@@ -897,9 +897,22 @@ void SimSetup::makeMolecules( void ){
     excludeOffset += info.nTorsions;
 
     
+    // send the arrays off to the forceField for init.
 
+    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
+    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
+    the_ff->initializeBends( info.nBends, info.myBends, theBends );
+    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
 
 
+    the_molecules[i].initialize( info );
+    atomOffset += info.nAtoms;
+  }
+
+  // clean up the forcefield
+
+  the_ff->cleanMe();
+}