diff -ru orig/AmberTools/src/ptraj/actions.c amber12/AmberTools/src/ptraj/actions.c
--- orig/AmberTools/src/ptraj/actions.c	2013-05-02 13:16:23.000000002 +0200
+++ amber12/AmberTools/src/ptraj/actions.c	2013-11-18 16:59:15.681119594 +0100
@@ -9309,7 +9309,7 @@
   int i, j, k, pt, iacceptor, iacceptorH, idonor, donors, acceptors, isolvent;
   int i1, i2, index, id, ia, idres, iares, found, current;
   double mem;
-  long kalloc;
+  size_t kalloc, li;
   int *sortindex;
   double a, d;
   double m;
@@ -10730,17 +10730,17 @@
     hbondInfo->distance2 = (float *) safe_malloc(sizeof(float) * k);
     hbondInfo->angle = (float *) safe_malloc(sizeof(float) * k);
     hbondInfo->angle2 = (float *) safe_malloc(sizeof(float) * k);
-    for (i=0; i < k; i++) {
-      hbondInfo->occupied[i] = 0.0;
-      hbondInfo->distance[i] = 0.0;
-      hbondInfo->distance2[i] = 0.0;
-      hbondInfo->angle[i] = 0.0;
-      hbondInfo->angle2[i] = 0.0;
+    for (li=0; li < k; li++) {
+      hbondInfo->occupied[li] = 0.0;
+      hbondInfo->distance[li] = 0.0;
+      hbondInfo->distance2[li] = 0.0;
+      hbondInfo->angle[li] = 0.0;
+      hbondInfo->angle2[li] = 0.0;
     }
 
     if (hbondInfo->series) {
 
-      kalloc = hbondInfo->series * donors * acceptors;
+      kalloc = (long)hbondInfo->series * donors * acceptors;
       if ( ( kalloc * sizeof(float) ) < 0 ) {
 	mem = (float) hbondInfo->series * (float) donors * (float) acceptors * (float) sizeof(float);
 	fprintf(stdout,"\n  WARNING in ptraj, hbond -- requesting allocation of a negative number of bytes!\n");
@@ -10752,10 +10753,10 @@
       hbondInfo->seriesDistance = (float *) safe_malloc( sizeof(float) * kalloc );
       hbondInfo->seriesAngle = (float *) safe_malloc( sizeof(float) * kalloc );
 
-      for (i=0; i < kalloc; i++) {
-	hbondInfo->seriesOccupied[i] = 0.0;
-	hbondInfo->seriesDistance[i] = 0.0;
-	hbondInfo->seriesAngle[i] = 0.0;
+      for (li=0; li < kalloc; li++) {
+	hbondInfo->seriesOccupied[li] = 0.0;
+	hbondInfo->seriesDistance[li] = 0.0;
+	hbondInfo->seriesAngle[li] = 0.0;
       }
     }      
   }