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

[Marc F. Lensink]

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