--- branches/new_design/OOPSE-4/src/UseTheForce/DUFF.cpp	2004/11/19 18:02:33	1759
+++ branches/new_design/OOPSE-4/src/UseTheForce/DUFF.cpp	2004/11/19 20:23:26	1760
@@ -76,7 +76,7 @@ void DUFF::parse(const std::string& filename) {
     std::string line;
     char buffer[bufferSize];
     int lineNo = 0;
-    int atomIdent = 1;  //atom's indent begins from 1 (since only fortran's array begins from 1)
+    int atomIdent = getNAtomType() + 1;  //atom's indent begins from 1 (since only fortran's array begins from 1)
     ParseState currentSection = DUFF::UnknownSection;
     
     while(ffStream.getline(buffer, bufferSize)){
@@ -198,10 +198,14 @@ void DUFF::parseAtomType(const std::string& line, int 
         atomType->setName(atomTypeName);
         atomType->setMass(mass);
         
-        //by default, all of the properties in AtomTypeProperties is set to 0
-        //In  Lennard-Jones Force Field, we only need to set Lennard-Jones to true
-        atomType->setLennardJones();
+        if (isLJ) {
+            atomType->setLennardJones();
+        }
 
+        if (isCharge) {
+            atomType->setCharge();
+        }
+        
         atomType->setIdent(ident); 
         
         atomType->complete();
@@ -261,9 +265,14 @@ void DUFF::parseDirectionalAtomType(const std::string&
 
         }
 
-        dAtomType->setDipole(isDipole);
-        dAtomType->setSticky(isSticky);
+        if (isDipole) {
+            dAtomType->setDipole();
+        }
 
+        if (isSticky) {
+            dAtomType->setSticky();
+        }
+        
         Mat3x3d inertialMat;
         inertialMat(0, 0) = Ixx;
         inertialMat(1, 1) = Ixx;