remarks changed Tue Sep  2 09:48:07 CDT 2003
remarks by jfd to include a fes residue

!@generate_tmoc.inp

topology reset end
structure reset end

topology 
{===>} @TOPPAR:topallhdg5.3.pro
end

! no chain id.
segment  name="    " 
    chain 
        @TOPPAR:topallhdg5.3.pep
        sequence
       		@1xxx.seq 
	end
    end 
    chain
       sequence
              ZIN
       end
    end
end

! removes the hydrogen on the cys-en
! and changes the atom type from SH1E to S.
!patch DISN reference=1=( resid 18 )
!           reference=2=( resid 21 ) 
!           end

! turn doubly protonated his to singly protonated histidine (HD1)
!patch HISD reference=nil=( resid 34 ) 
!           reference=nil=( resid 40 ) 
!           end

patch ZINC
     reference=1=( resid 18 )
     reference=2=( resid 21 )
     reference=3=( resid 34 )
     reference=4=( resid 40 )
     reference=5=( resid 68 )
end

! turn peptide from trans to cis
!patch CISP reference=nil=( resid 80 ) end


evaluate ( $par_nonbonded = "OPLSX" )
parameter reset end

parameter @TOPPAR:parallhdg5.3.pro 
end

!coor @1xxx_xplor.pdb

! show everything is consistent (or not)
!energy end
!  print thres=0.05 bonds
!  print thres=5. angles
!  print thres=5. impropers
!  print thres=140 dihe

!coor init sele  ( all  ) end


write psf       output=1xxx.psf end
stop

! junk not reached by script. 
 
  print thres=0.05 bonds
  print thres=5. angles
  print thres=0.5 impropers
  print thres=140 dihe