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.
Cheers,
Tsjerk
On 1/12/07, Marc F. Lensink <[EMAIL PROTECTED]> 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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