Hi all, I want to generate a disulphide bond between two cysteine residues of two monomers of a protein, to create a dimer protein. But, it is not happening while running the pdb2gmx, because there is TER record at the end of one monomer subunit pdb file. However, using the -chainsep option and defining the two monomers as a single molecule generate the disulphide bond but cause the formation of peptide bond between the two terminal ends of monomer chains. Please let me know, if there is any other way to make intermolecule disulphide bond, without linking the two monomers ends with peptide bond.
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