Hi Adriana,<br>
<br>
pdb2gmx should be able to detect SS bonds automatically, though in some
cases fails to do so (if the distance is too large). If you know that
you're missing a SS bond you can add an entry to the file specbond.dat
in the directory $GMXDIR/share/top (maybe first copy the file to your
directory). Copy the line referring to the cys-bridge and change the
distance to the distance in your structure. Running through pdb2gmx
should then fix your problem.<br>
<br>
With regards to the other issue, neither editconf nor genbox changes
your structure (there's no cutting). There may be shifts over the
periodic boundaries, but these don't affect the resulting simulation
system.<br><br>
Cheers,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 11/29/05, <b class="gmail_sendername">Adriana Pietropaolo</b> <<a href="mailto:adriana@ms.fci.unibo.it">adriana@ms.fci.unibo.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>I was curious about gromacs package and so I would try to make a dynamics<br>with our package.<br>I had some problem with the CYS residue, because if I insert CYS2 the<br>pdb2gmx read CYSH, but if I change in my parameter file the residue with
<br>the name CYX as CYS, the topology generated is with the group of protein<br>and with this CYX group.<br>Furthermore, I already had a box, but I don't know why the topology<br>contains three solvent group, like SOL SOL SOL.
<br>If I try to generate a box with editconf and genbox, this procedure cuts<br>my my protein bonds.<br>How can I do?<br>Thanks in advance,<br>Adriana<br><br>--<br>_____________________________________________<br>Adriana Pietropaolo,
<br>PhD student,<br>dipartimento di Chimica Fisica ed Inorganica,<br>Facolta' di Chimica Industriale<br>Universita' di Bologna<br>Tel 051/6446992<br>FAX 051/2093690<br>_____________________________________________<br><br>
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<br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
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