diff -Naur lammps-1Nov09/src/MOLECULE/angle_hybrid.cpp lammps-2Nov09/src/MOLECULE/angle_hybrid.cpp
--- lammps-1Nov09/src/MOLECULE/angle_hybrid.cpp	2009-01-05 15:26:08.000000000 -0700
+++ lammps-2Nov09/src/MOLECULE/angle_hybrid.cpp	2009-10-30 13:53:21.000000000 -0600
@@ -73,8 +73,10 @@
 
   if (neighbor->ago == 0) {
     for (m = 0; m < nstyles; m++) nanglelist[m] = 0;
-    for (i = 0; i < nanglelist_orig; i++)
-      nanglelist[map[anglelist_orig[i][3]]]++;
+    for (i = 0; i < nanglelist_orig; i++) {
+      m = map[anglelist_orig[i][3]];
+      if (m >= 0) nanglelist[m]++;
+    }
     for (m = 0; m < nstyles; m++) {
       if (nanglelist[m] > maxangle[m]) {
 	memory->destroy_2d_int_array(anglelist[m]);
@@ -86,6 +88,7 @@
     }
     for (i = 0; i < nanglelist_orig; i++) {
       m = map[anglelist_orig[i][3]];
+      if (m < 0) continue;
       n = nanglelist[m];
       anglelist[m][n][0] = anglelist_orig[i][0];
       anglelist[m][n][1] = anglelist_orig[i][1];
diff -Naur lammps-1Nov09/src/MOLECULE/bond_hybrid.cpp lammps-2Nov09/src/MOLECULE/bond_hybrid.cpp
--- lammps-1Nov09/src/MOLECULE/bond_hybrid.cpp	2009-01-05 15:26:08.000000000 -0700
+++ lammps-2Nov09/src/MOLECULE/bond_hybrid.cpp	2009-10-30 13:53:21.000000000 -0600
@@ -73,8 +73,10 @@
 
   if (neighbor->ago == 0) {
     for (m = 0; m < nstyles; m++) nbondlist[m] = 0;
-    for (i = 0; i < nbondlist_orig; i++)
-      nbondlist[map[bondlist_orig[i][2]]]++;
+    for (i = 0; i < nbondlist_orig; i++) {
+      m = map[bondlist_orig[i][2]];
+      if (m >= 0) nbondlist[m]++;
+    }
     for (m = 0; m < nstyles; m++) {
       if (nbondlist[m] > maxbond[m]) {
 	memory->destroy_2d_int_array(bondlist[m]);
@@ -86,6 +88,7 @@
     }
     for (i = 0; i < nbondlist_orig; i++) {
       m = map[bondlist_orig[i][2]];
+      if (m < 0) continue;
       n = nbondlist[m];
       bondlist[m][n][0] = bondlist_orig[i][0];
       bondlist[m][n][1] = bondlist_orig[i][1];
diff -Naur lammps-1Nov09/src/MOLECULE/dihedral_hybrid.cpp lammps-2Nov09/src/MOLECULE/dihedral_hybrid.cpp
--- lammps-1Nov09/src/MOLECULE/dihedral_hybrid.cpp	2009-01-05 15:26:08.000000000 -0700
+++ lammps-2Nov09/src/MOLECULE/dihedral_hybrid.cpp	2009-10-30 13:53:21.000000000 -0600
@@ -73,8 +73,10 @@
 
   if (neighbor->ago == 0) {
     for (m = 0; m < nstyles; m++) ndihedrallist[m] = 0;
-    for (i = 0; i < ndihedrallist_orig; i++)
-      ndihedrallist[map[dihedrallist_orig[i][4]]]++;
+    for (i = 0; i < ndihedrallist_orig; i++) {
+      m = map[dihedrallist_orig[i][4]];
+      if (m >= 0) ndihedrallist[m]++;
+    }
     for (m = 0; m < nstyles; m++) {
       if (ndihedrallist[m] > maxdihedral[m]) {
 	memory->destroy_2d_int_array(dihedrallist[m]);
@@ -87,6 +89,7 @@
     }
     for (i = 0; i < ndihedrallist_orig; i++) {
       m = map[dihedrallist_orig[i][4]];
+      if (m < 0) continue;
       n = ndihedrallist[m];
       dihedrallist[m][n][0] = dihedrallist_orig[i][0];
       dihedrallist[m][n][1] = dihedrallist_orig[i][1];
diff -Naur lammps-1Nov09/src/MOLECULE/improper_hybrid.cpp lammps-2Nov09/src/MOLECULE/improper_hybrid.cpp
--- lammps-1Nov09/src/MOLECULE/improper_hybrid.cpp	2009-01-05 15:26:08.000000000 -0700
+++ lammps-2Nov09/src/MOLECULE/improper_hybrid.cpp	2009-10-30 13:53:21.000000000 -0600
@@ -73,8 +73,10 @@
 
   if (neighbor->ago == 0) {
     for (m = 0; m < nstyles; m++) nimproperlist[m] = 0;
-    for (i = 0; i < nimproperlist_orig; i++)
-      nimproperlist[map[improperlist_orig[i][4]]]++;
+    for (i = 0; i < nimproperlist_orig; i++) {
+      m = map[improperlist_orig[i][4]];
+      nimproperlist[m]++;
+    }
     for (m = 0; m < nstyles; m++) {
       if (nimproperlist[m] > maximproper[m]) {
 	memory->destroy_2d_int_array(improperlist[m]);
@@ -87,6 +89,7 @@
     }
     for (i = 0; i < nimproperlist_orig; i++) {
       m = map[improperlist_orig[i][4]];
+      if (m < 0) continue;
       n = nimproperlist[m];
       improperlist[m][n][0] = improperlist_orig[i][0];
       improperlist[m][n][1] = improperlist_orig[i][1];