[gmx-users] big protein dynamics with gromacs 3.2.1

[Adriana Pietropaolo]

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

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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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