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

[Luca Mollica]

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.

Thanks in advance & Bye

LM




___________________________________________________________________

Luca Mollica
Biomolecular NMR Laboratory 1B4
Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute
Via olgettina 58
20132 Milano
Italy

Tel: 0039-0226433497/4922
Fax: 0039-0226434153

Il futuro non è più quello di una volta
(A.D. Clarke)