Dear Gromacs users, Is there any way to handle the disulphide bond formed between two independent fragments of a protein ? Precisely it is an inter disulphide bond between two fragments. If I keep the two fragments as separate objects while preparing the pdb file (using TER between the two fragments), gromacs is not asking for the formation of a disulphide bond. If I keep them as a single object while preparing the input pdb, gromacs could recognize the disulphide bond but while running the energy minimization its complaining that the distances are too close.
Is there any way to handle these ? I am also thinking like keep them as separate objects and imposing positional restraints on both the sulphur atoms. Is it all right to do that way ? Please suggest me some thing how to handle these ? Ram.
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