[gmx-users] procedure for creating an S-S bridge

[OZGE ENGIN]

Hi all,

I want to create an S-S bond within my peptide. So, I used the CYSH type cysteine residue and pdb2gmx with -ss option. However, I saw that the S-S bridge was formed between the ARG-CYS pair but not between the CYS-CYS pair. 

So, I think -ss option with pdb2gmx is not enough to make this bond. What additional steps do I follow to construct this bond ? 

Thanks in advance
Ozge Engin
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Computational Science & Engineering
Koc University