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disulfide in a single chain

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  • andrea
    Hi all, I am new in cns. this is a just a curiosity. I have a small sequence of a peptide with two CYS in position 1 and 5. I d like to make a disulfide bond
    Message 1 of 1 , May 3, 2006
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      Hi all,
      I am new in cns. this is a just a curiosity. I have a small sequence
      of a peptide with two CYS in position 1 and 5. I'd like to make a
      disulfide bond between them and so in genereate_seq.inp I add:
      {+ choice: true false +}
      {===>} ss_use_1=true;
      {===>} ss_i_segid_1="A"; ss_i_resid_1=1;
      {===>} ss_j_segid_1="A"; ss_j_resid_1=5;

      Everything runs fine, the mtf file contains the information about the
      bond S-S. However afterwards generate_extended.inp generateds a pdb
      file which doesn't contain S-S bond (visualizing it in vmd or pymol).
      I should expect a cycle rather than an "extended" peptide. Is it
      normal? Thank for any explanation

      Regards

      andrea
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