cd $AMBERHOME
patch -p0 -N < patch 

Author: Daniel R. Roe
Date: 2010-07-26
Description:
Fixes two bugs in clustering code: 1) If no atoms are selected in RMS mask 
resulting NULL mask, segfault would occur or 2) Pointer was being compared
like an integer; the check would result in no initialization and a segfault.
-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/actions.c	2010-07-26 09:30:41.462276836 -0400
+++ AmberTools/src/ptraj/actions.c	2010-07-26 09:31:36.767408649 -0400
@@ -3655,6 +3655,8 @@
         {
             action->mask = processAtomMask("*", action->state);
         }
+        if (action->mask==NULL) 
+          return INVALID_ARGUMENTS_RETURN_CODE;
         /* Create a new "substate" trajInfo->state containing only some atoms: */
         modifyStateByMask(&trajInfo->state, &action->state, action->mask, 0);
         trajInfo->atoms = trajInfo->state->atoms;
--- AmberTools/src/ptraj/cluster.c	2010-07-26 22:48:49.998157908 -0400
+++ AmberTools/src/ptraj/cluster.c	2010-07-26 22:51:04.023535647 -0400
@@ -4041,7 +4041,7 @@
 		OutputTrajInfo = (trajectoryInfo*)action->carg2;
     }
 
-    if (!FirstOutputFlag)
+    if (FirstOutputFlag==NULL)
     {
       FirstOutputFlag = (int*)SafeMalloc(__FILE__, __LINE__, sizeof(int) * This->ClusterCount);
       memset(FirstOutputFlag, 1, sizeof(int) * This->ClusterCount);