Hi,
I have a problem with Gromacs. I want to do MD simulations with my proteïn in a
DPPC-membrane.
Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I
just used a bigger
membrane (256 lipids instead of 128). I managed to correctly embed the proteïn
in the bilayer,
I solvated it with genbox and then I want to add ions. But when I use grompp to
get a .tpr
file for genion, Gromacs fives the following error:
Program grompp, VERSION 4.0.7
Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320
Fatal error:
No molecules were defined in the system
I did update my topology in the [ molecules ] section and checked it twice to
see if it fits with
the .gro file. It is correct, so I don't know what the problem is. Before the
solvation there was
no problem with grompp, so it must have something to do with the solvation? I
hope someone
can help me.
Thanks,
Marysa van den Berg
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