[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 27 15:43:43 CET 2003

On Mon, 2003-01-27 at 13:32, 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 run pdb2gmx on the protein only, and edit the resulting topology
manually to include the lipids and water etc.

Description in chapter 5 of the manual.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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