Revert Amber-MD#1159

Author: Daniel R. Roe

src/Parm_Amber.cpp

@@ -890,7 +890,7 @@ int Parm_Amber::ReadLJC(Topology& TopIn, FortranData const& FMT) {
   if (SetupBuffer(F_LJ_C, numLJparm_, FMT)) return 1;
   for (int idx = 0; idx != numLJparm_; idx++)
   {
-    TopIn.SetNonbond().SetLJC( idx, FileBufferToDouble(F_LJ_C, idx, numLJparm_) );
+    TopIn.SetNonbond().AddLJC( FileBufferToDouble(F_LJ_C, idx, numLJparm_) );
     if (atProblemFlag_) break;
   }
   return 0;
@@ -2094,7 +2094,6 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
 
   // LJ A and B terms
   if (WriteLJ(F_LJ_A, F_LJ_B, TopOut.Nonbond().NBarray())) return 1;
-
 
   // CHAMBER only - LJ 1-4 terms
   if (ptype_ == CHAMBER) {
@@ -2481,10 +2480,10 @@ int Parm_Amber::WriteParm(FileName const& fname, Topology const& TopOut) {
   // LJ C terms.
   // NOTE: I put this at the very end to match behavior of parmed add_12_6_4
   if (TopOut.Nonbond().Has_C_Coeff()) {
-    if (BufferAlloc(F_LJ_C, TopOut.Nonbond().NBarray().size())) return 1;
-    for (NonbondArray::const_iterator it = TopOut.Nonbond().NBarray().begin();
-                                      it != TopOut.Nonbond().NBarray().end(); ++it)
-      file_.DblToBuffer( it->C() );
+    std::vector<double> const& ccoef = TopOut.Nonbond().LJC_Array();
+    if (BufferAlloc(F_LJ_C, ccoef.size())) return 1;
+    for (std::vector<double>::const_iterator it = ccoef.begin(); it != ccoef.end(); ++it)
+      file_.DblToBuffer( *it );
     file_.FlushBuffer();
   }