[gmx-users] (no subject)

[Bert de Groot]

Itamar Kass wrote:
> 
> Ho wise advisories, I am trying to use the lipid and DMPC files from Dr. Tieleman site, I also downloaded the file ffgmx_lipids.tar.gz from the gromacs home-page and opened it. The problem is that I do not know how to implement thus files in my molecule, I understand that I have to include the dmpc.itp and lipid.itp files in the topology file for the system, but I can not produce the topology file using pdb2gmx.

you don't need pdb2gmx for the lipids. Just include the ffgmx.itp from the
ffgmx_lipids.tar.gz (which also defines the params from lipid.itp, so that
you don't need to include lipid.itp anymore). Then include dmpc.itp and you're
ready to run.

your topology could look something like this:

#include "./ffgmx.itp"
#include "dmpc.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; Name
DMPC in water

[ molecules ]
; Compound        #mols
DMPC    271
SOL    4238


--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________