[gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits

[bipin singh]

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.



*-------------------Thanks and Regards,Bipin Singh*