[gmx-users] glutathionylation and SS bonds formation in GMX

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Jan 14 09:01:18 CET 2007

Hi Luca,

As Marc mentioned, they have to be recognized as one molecule
(-merge). In addition, it is not just that the distance has to be less
than that given in the specbond.dat file, it has to fall within a 10%
range aruond that distance.



On 1/12/07, Marc F. Lensink <lensink at scmbb.ulb.ac.be> wrote:
> On Fri, Jan 12, 2007 at 04:08:47PM +0100, Luca Mollica wrote:
> > Dear GMX users,
> >
> > I am trying to simulate a post translational modification of a protein,
> > actually a glutathionylation of a Cys. I have tried a couple of times to
> > create a disulphide bridge between two Cys and I managed to do it without
> > troubles and simply manipulating a specond.dat file created in my working
> > directory. But in this case I am experiencing a slightly different trouble!
> > The Glutathione (GSH) has been built in Pymol manually (Cys + Gly + Glu)
> > and the coordinates have been saved for keeping it close to the desired
> > Cys, with S - S distance less than how indicated in specbond.dat). So far
> > so good, everything in molecular structure was OK ... the troubles started
> > using GMX, when the two Cys were recognized, specbond.dat was read
> > correctly, but no bond was created. Actually, the protein and GSH remained
> > separated and there was no chance to make them bound through a disulphide
> > bridge. I even tried to give a cahin identifier to protein (A) and GSH (B),
> > but I got the same result: two separated units, no SS bond !
> >
> > Do you have any suggestion about this issue ? I am pretty sure that in the
> > past I got a certain degree of success because the Cys considered were part
> > of the same molecule, actually. But I cannot get the point for this failure
> > in the system building process.
> isn't there some option to merge (-merge) molecules in pdb2gmx?  i
> suppose you should also make sure that the atoms have the correct
> names.
> cheers,
> marc
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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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