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

Marysa van den Berg mvdberg1986 at hotmail.com
Thu Jan 28 12:27:34 CET 2010



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
Alles over Windows
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