Example: Incorporation of Disulfide Bridges

All protein force fields have the DISU patch residue defined. To make a disulfide bridge, one should use the patch statement; e.g.,

topology 
   presidue DISU     
      group
      modify atom 1CB           charge= 0.19  END
      modify atom 1SG  type=S   charge=-0.19  END
      group
      modify atom 2CB           charge= 0.19  END
      modify atom 2SG  type=S   charge=-0.19  END
      add bond 1SG 2SG
      add angle  1CB 1SG 2SG
      add angle  1SG 2SG 2CB
      add dihedral   1CA 1CB 1SG 2SG
      add dihedral   1CB 1SG 2SG 2CB
      add dihedral   1SG 2SG 2CB 2CA
   end 
end

patch
   reference=1=( resid 15 ) reference=2=( resid 25 ) 
end

will make a disulfide bridge between residue number 15 and residue number 25. (For completeness, the definition of the patch residue DISU is listed here as well. Normally, this patch residue is already included in the topology files.)