--- mdread.f	2006-04-03 16:35:55.000000000 -0700
+++ mdread.f	2006-06-25 16:42:14.000000000 -0700
@@ -2009,24 +2025,24 @@
             x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
    end if
    
-   if( ibelly > 0 .and. igb > 0 ) then
-      
-      !          ---here, the only allowable belly has just the first
-      !             NATBEL atoms in the moving part.  Check to see that this
-      !             requirement is satisfied:
-      
-      do i=natbel+1,natom
-         if( ix(ibellygp+i-1) /= 0 ) then
-            write(6,*) 'When igb>0, the moving part must be at the'
-            write(6,*) '   start of the molecule.  This does not seem'
-            write(6,*) '   to be the case here.'
-            write(6,*) 'natbel,i,igroup(i) = ' &
-                  ,natbel,i,ix(ibellygp+i-1)
-            call mexit(6,1)
-         end if
-      end do
-   end if
-   
+!   if( ibelly > 0 .and. igb > 0 ) then
+!      
+!      !          ---here, the only allowable belly has just the first
+!      !             NATBEL atoms in the moving part.  Check to see that this
+!      !             requirement is satisfied:
+!      
+!      do i=natbel+1,natom
+!         if( ix(ibellygp+i-1) /= 0 ) then
+!            write(6,*) 'When igb>0, the moving part must be at the'
+!            write(6,*) '   start of the molecule.  This does not seem'
+!            write(6,*) '   to be the case here.'
+!            write(6,*) 'natbel,i,igroup(i) = ' &
+!                  ,natbel,i,ix(ibellygp+i-1)
+!            call mexit(6,1)
+!         end if
+!      end do
+!   end if
+    write (6,'(''| WARNING: This version of AMBER has been customized by Ross Walker and Mike Crowley. It is unsupported and you use it at your own risk'')') 
 
    !     ----- CALCULATE THE SQUARE OF THE BOND PARAMETERS FOR SHAKE
    !           THE PARAMETERS ARE PUT SEQUENTIALLY IN THE ARRAY CONP -----
--- egb.f	2006-04-03 16:35:54.000000000 -0700
+++ egb.f	2006-06-25 15:26:19.000000000 -0700
@@ -104,7 +104,7 @@
 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 !+ handles generalized Born functionality, plus reg. nonbon, plus surface area
 subroutine egb(x,f,rborn,fs,reff,onereff,charge,iac,ico,numex, &
-      natex,dcharge,cut,ntypes,natom,natbel, &
+      natex,dcharge,cut,ntypes,natom,natbel,gbbellymask, &
       epol,eelt,evdw,esurf,dvdl,vdwrad,ineighbor,p1,p2,p3,p4, &
       rbmax,rbmin,rbave,rbfluct,ncopy )
    
@@ -238,6 +238,7 @@
    integer iac,ico,numex,natex,ntypes,natom,natbel,ncopy
    integer i,j,k,kk1,maxi,num_j_vals,jjj,count2_fin,num_k_vals, &
            iexcl,iaci,jexcl,jexcl_last,jjv,ic,kk
+   integer gbbellymask(natom)
    integer j3
    integer loop_count
 #ifdef MPI
@@ -425,7 +426,7 @@
 #endif
 
    maxi = natom
-   if(natbel > 0) maxi = natbel
+!   if(natbel > 0) maxi = natbel
 
    !--------------------------------------------------------------------------
    !
@@ -452,9 +453,6 @@
 
    nnbips = 0
    call timer_start(TIME_GBFRC)
-   
-   !       Note: this code assumes that the belly atoms are the first natbel
-   !             atoms...this is checked in mdread.
 
 #ifdef MPI
    do i=mpistart,maxi,numtasks
@@ -462,7 +460,19 @@
    
    do i=1,maxi
 #endif
-
+      !If belly skip
+      if (natbel > 0) then
+         if (gbbellymask(i) == 0) then
+#ifdef MPI
+           do k=i,(min(i+numtasks-1,natom))
+             iexcl = iexcl + numex(k)
+           end do
+#else
+           iexcl = iexcl + numex(i)
+#endif
+           cycle
+         end if
+      end if
 #ifdef PIMD
       lestmp = nlesty*(lestyp(i)-1)
 #endif
@@ -925,7 +935,6 @@
             !we can use the cached values.
             rinv = vectmp5(k) !1/rij
             r2inv = rinv*rinv
-         
             if( doeel ) then
 #ifdef LES
                eel = intdieli*qiqj*rinv*lesscalefac(k)
@@ -1143,6 +1152,10 @@
 #else
       do i=1,maxi
 #endif
+         !If belly skip
+         if (natbel > 0) then
+            if (gbbellymask(i) == 0) cycle
+         end if
          
          f_xi = zero
          f_yi = zero
@@ -1731,6 +1744,10 @@
 #else
        do j=1,maxi !1 to natom
 #endif
+         !If belly skip
+         if (natbel > 0) then
+            if (gbbellymask(i) == 0) cycle
+         end if
          !Do all atoms that are not excluded and
          !are within the cutoff for this i. Skip other 
          !MM interactions that are less than i to avoid double
--- force.f	2006-04-03 16:35:55.000000000 -0700
+++ force.f	2006-06-24 14:21:20.000000000 -0700
@@ -754,7 +754,7 @@
       call timer_start(TIME_EGB)
       call egb( x,f,rborn,fs,reff,onereff,xx(l15),ix(i04),ix(i06), &
             ix(i08),ix(i10),xx(l190), &
-            cut,ntypes,natom,natbel,epol,eelt,evdw, &
+            cut,ntypes,natom,natbel,ix(ibellygp),epol,eelt,evdw, &
             esurf,dvdl,xx(l165),ix(i82),xx(l170),xx(l175),xx(l180), &
             xx(l185), xx(l186),xx(l187),xx(l188),xx(l189),ncopy )