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)
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