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

[Mark Abraham]

> 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.

That's not possible with the unmodified form of specbond.dat - you are
probably seeing a visualization artefact
http://wiki.gromacs.org/index.php/Trajectory_Visualisation#Topology_bonds_vs_Rendered_bonds.

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

Check out http://wiki.gromacs.org/index.php/specbond.dat

Mark