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

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 28 13:05:20 CET 2010

Do you have the right number of atoms indicated on the second line of the .gro 
file?  What is in your [molecules] directive in your topology?


Marysa van den Berg 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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