[gmx-users] grompp gives "no molecules were defined in the system"

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 28 13:04:23 CET 2010

Hi Marysa,

The error is about the definition of mulecules, which suggests that
there are no [ moleculetype ] directives. Did you #include the proper
.itp file(s) with the necessary moleculetype definitions? If not,
you'll have to provide more information, probably posting the topology
file itself.



On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg
<mvdberg1986 at hotmail.com> wrote:
> 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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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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