Dear sir, I want to create S-S bond between two cys in a peptide chain irrespective of the conformation of the peptide. I tried this using an option -ss as flag in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more in free cysSH cysSH, but i want to bring them together to form S-S bond. Plz tell me so that i could solve my problem?
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