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".
Cheers,
Stéphane
--
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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