[gmx-users] grompp error in peptide-membrane simulations

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Mar 3 10:33:13 CET 2007

Hi Maite,

Indeed you shouldn't really run the lipids through pdb2gmx, but try to
obtain a .itp file for a lipid, matching the force field you're trying
to use. What you can do is take one lipid and run it through pdb2gmx,
using your favourite force field. Make sure that the resulting
structure file is not different in terms of the number of atoms and
the order of them. Then you can use #include "lipid_ffG53a5.itp" in
your .top file and under system list the number of lipids you have in
your structure file. It may be a good idea to edit the
lipid_ff53a6.itp file and change the name of the molecule. I hope I'm
a bit clear, but in case I'm not, I think that you have to do
additional reading of the manual in order to understand the topology
files (chapter 5) until you grasp the idea. Now, to summarize a bit:

1. Construct the topology for your protein using pdb2gmx+ffG53a5
2. Extract one lipid from lipid.pdb and run it through pdb2gmx+ffG53a5
3. Modify the resulting .top file from #2 to make it a .itp file (a
molecule definition)
4. Set up the system consisting of the protein and the lipids (and
make sure that all the lipids are whole, i.e. not split over the
periodic boundaries)
5. construct the topology for the system by adding the lipid topology
to the protein.top file.

Hope it helps,


On 3/3/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> maite lopez wrote:
> > i've changed the atoms of the dppc.itp  file by the atoms of the DPPC
> > molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3)
> > and run grompp , but it gives :
> > Fatal error:
> > Atomtype 'C1' not found!
> >
> > I don´t  know  how  to convert my  lipids to ffG53a5. Could you
> > explain me briefly?
> So find where C1 is being referenced, and whether it should be being
> defined elsewhere, and if it isn't defined work out why it isn't.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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