[gmx-users] big protein dynamics with gromacs 3.2.1
adriana at ms.fci.unibo.it
Tue Nov 29 14:41:34 CET 2005
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,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
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