remarks re_h2o.inp (derived from sa_l.inp)
!     ************************************
!     * Authors and copyright:           *
!     * Michael Nilges, Jens Linge, EMBL *
!     * No warranty implied or expressed *
!     * All rights reserved              *
!     ************************************

evaluate ($structure = "protein.psf")
evaluate ($file = "the_coords.pdb")

topology  
    @@topallhdg5.2.pro
    @@topallhdg.sol
end 

evaluate ($par_nonbonded = "OPLSX")

!load the parameter files:
parameter 
  @@parallhdg5.2.pro
  @@parallhdg.sol
  nbonds
    nbxmod=5 atom cdiel shift 
    cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25
    wmin=0.5
    tolerance  0.5
  end
end


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! think of the ss bonds!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

{ ! for ambiguous SS bonds 
parameter  nbfix S  S  462  13.6  462  13.6 end
}

evaluate ($kcdih = 5)
restraints dihedral 
      scale=$kcdih
end 


evaluate ($seed = 3889876655332)
set seed $seed end

@h2orefine.cns

evaluate ($filename= $file -  ".pdb" + "w.pdb")

write coordinates sele= (not resn TIP3) output =$filename end
      
stop