Re: Lipids into NAMD

From: Alessandro Cembran (cembran_at_chem.umn.edu)
Date: Mon Aug 21 2006 - 10:21:02 CDT

The Benoit Roux lab has libraries of pre-equilibrated DMPC and DPPC in
CHARMM format.

http://thallium.bsd.uchicago.edu/RouxLab/membrane.html

You can easily read them with VMD and then save them as pdb. Some lipids
are already present in the CHARMM topology file as a whole, others need
to be built by patching together tails and polar head.

You can find the topology and parameter files here:

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

If you have access to the CHARMM program, you can build basically any
type of lipids you want, by patching the existing tails and polar heads
together. If the patch you need doesn't exist in the topology file, you
can always create your own. You save then the psf file in xplor format
and use that for namd.

Hope this helps,

Alessandro

Lechuga, Javier wrote:
> Hello,
>
> In order to model lipids, different from POPC and POPE, into NAMD, I need Pdb, topology and parameter files for these molecules. Does anyone know where could I find those?
>
> Thank you
>
>

-- 
Alessandro Cembran,PhD
Post Doctoral Associate
Univ. of Minnesota, Dept. of Chemistry
G2, 139 Smith Hall 207 Pleasant St SE
Minneapolis, MN 55455-0431
Office: +1 612-625-4319
cembran_at_chem.umn.edu

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