[gmx-users] pdbgmx warning long bond

Stéphane Téletchéa steletch at jouy.inra.fr
Fri Jan 26 11:09:26 CET 2007

maite lopez a écrit :
> Dear Gromacs Users,
> I am trying to simulate a peptide in explicit lipid bilayer membrane
> environment (say, DPCC). I took well equilibrated dppc.pdb file from
> Dr. Peter tieleman site and  i modified it put in the names of the
> atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp
> file. But when  executing pdb2gmx ( pdb2gmx_331 -f input.pdb -o
> output.gro -p output.top -i output.itp -ffG53a5 -water spc -ignh) i
> 've gived some errors.
> The long bonds are in the atoms of the membrane. Why it could be?
> Could anybody give me a pointer to a  more elaborated protocol in
> setting up and running this type of  simulation using gromacs? This is
> my first simulation.

I assume you're using Dr. Tieleman's lipids ...
The problem comes from the imaging of the lipids, since if you look 
closely, you'll see some lipids are starting on one side of the box and 
terminates on the other side.

I've explained in detail how to proceed to correct this, please have a 
look at my message from "30.11.2006 17:57".



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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