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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
