[gmx-users] protonated cys -S

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 10 11:47:01 CET 2006

Hi Giacomo,

The two sulphur atoms have to be at a proper distance to be recognized
as involved in a S-S bond. In your case, if you're certain that there
should be a bond, you have to edit the file specbond.dat, find the
entry which links two cysteine residues and set the distance to the
actual distance in your structure (there is a 10% margin).

Hope it helps,


On 11/10/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
> Dear users,
> I have just found that gromacs protonate the -S of
> my Cys and I would like to have it deprotonated
> to form a disulphide bond (It is present in the original
> pdb file).
> Is there any way I can modify it?
> thanks in advance,
> Giacomo
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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