[gmx-users] S-S Bonds

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 2 13:26:53 CEST 2007

Hi Roberto,

> I want to do MD of insulin monomer (first two chain of 4ins.pdb). When I
> convert with pdb2gmx, the software find only one ss bond (the only inside
> the same chain). I have resolved this problem doing a first conversion
> pdb->gro, then gro->pdb end in the final conversion pdb->gro the software
> find the all three ss bond, and number the residues of the two chain like
> one.

You should check my post from this morning on another thread about SS
bonds (hint: pdb2gmx option -merge).
Also, your pdb -> gro -> pdb -> gro conversions don't change anything.
You also can't infer from the structure in a viewer whether you have
an SS bond listed in the topology. The topology is a different thing.

> But now there is the big problem, when I do a two step minimization (for bad
> contacts) the two chain go away, like no ss bonds exist.

Because there is no SS bond...; see above.

> Whit VMD I can see that all the S atoms is on one chain (the first, whit
> have the internal SS bond). Then there are two CYS with two S atoms and two
> (on the other chain) with no S atom.
> I have cecked the topology file, and the bond between CB and S, and S-S  are
> all correct.
> I think that the problem is inside the two chain configuration, but I
> haven't explanation for the CYS without S.

I haven't got a clue on your 'CYS without S', but you are right that
the other part has to do with having two chains...

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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