[gmx-users] S-S Bonds

[Tsjerk Wassenaar]

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

-- 
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