[gmx-users] big protein dynamics with gromacs 3.2.1

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 29 16:36:58 CET 2005

Hi Adriana,

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

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.



On 11/29/05, Adriana Pietropaolo <adriana at ms.fci.unibo.it> wrote:
> Hi,
> I was curious about gromacs package and so I would try to make a dynamics
> with our package.
> I had some problem with the CYS residue, because if I insert CYS2 the
> pdb2gmx read CYSH, but if I change in my parameter file the residue with
> the name CYX as CYS, the topology generated is with the group of protein
> and with this CYX group.
> Furthermore, I already had a box, but I don't know why the topology
> contains three solvent group, like SOL SOL SOL.
> If I try to generate a box with editconf and genbox, this procedure cuts
> my my protein bonds.
> How can I do?
> Thanks in advance,
> Adriana
> --
> _____________________________________________
> Adriana Pietropaolo,
> PhD student,
> dipartimento di Chimica Fisica ed Inorganica,
> Facolta' di Chimica Industriale
> Universita' di Bologna
> Tel 051/6446992
> FAX 051/2093690
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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