[gmx-users] grompp gives "no molecules were defined in the system"
tsjerkw at gmail.com
Thu Jan 28 13:04:23 CET 2010
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
On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg
<mvdberg1986 at hotmail.com> wrote:
> 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.
> Marysa van den Berg
> Minder SPAM in de verbeterde Windows Live Hotmail
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Tsjerk A. Wassenaar, Ph.D.
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