[gmx-users] lipid.itp and GROMACS versions

Luca Mollica mollica.luca at hsr.it
Thu Sep 4 12:11:02 CEST 2003

Dear all users,

I've encountered a problem trying to simulate a protein-membrane simulation.

a) Being recently a visitor in another laboratory than mine, I've prepared all 
the files for the simulation and run the simulation itself on GROMACS 3.0.5, 
and everything was fine, without any troubles: I've built the system using 
GROMACS force field and run the simulation including all the following files:


b) Returning to my lab(I use GROMACS 3.1.4), I've tried to run the same kind 
of simulation using the same set of files. But the grommp step was broken 
reporting this error:

calling /lib/cpp...
processing topology...
WARNING 2 [file "lipid.itp", line 13]:
  Overriding atomtype LO
WARNING 3 [file "lipid.itp", line 14]:
  Overriding atomtype LOM
WARNING 4 [file "lipid.itp", line 15]:
  Overriding atomtype LNL
WARNING 5 [file "lipid.itp", line 16]:
  Overriding atomtype LC
WARNING 6 [file "lipid.itp", line 17]:
  Overriding atomtype LH1
WARNING 7 [file "lipid.itp", line 18]:
  Overriding atomtype LH2
WARNING 8 [file "lipid.itp", line 19]:
  Overriding atomtype LP
WARNING 9 [file "lipid.itp", line 20]:
  Overriding atomtype LOS
WARNING 10 [file "lipid.itp", line 21]:
  Overriding atomtype LP2
Cleaning up temporary file grompp7t0UeH
Fatal error: Too many warnings, grompp terminated

Then, not including the lipid.itp file, the grompp operation was no longer 
interrupted and I had success with my simulation.

Does anyone have ny kind of suggestion for this problem? Could it be related 
to different GROMACS versions? How is it possible to solve the problem??

Thank you in advance




Luca Mollica
Dulbecco Telethon Institute (Protein Structure Laboratory)
c/o Cellular and Molecular Neurobiology
DIBIT-HSR,Via Olgettina 58
20132 Milano (Italy)

Tel: 0039-02-26434824
Fax: 0039-02-26434813
E-mail: mollica.luca at hsr.it

DTI website: http://www.telethon.it/dti/

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