Re: Generate psf files from Scott Feller's lipid coordinates

From: Jeffrey Potoff (
Date: Sun May 16 2010 - 01:35:23 CDT

Dai, Jian1 wrote:
> Hi, NAMD users:
> We're trying to simulate bilayers of different lipids, (DPPC, POPC, etc), with different size, (72, 128, etc).
> On Dr. Scott Feller's website there are some bilayer coordinates, but I don't know how to generate the necessary psf files from those pdb files. Can someone tell us how to do this?
> Thank you.
> Jian
The general idea of generating PSF files from PDB files is explained in
the NAMD tutorials. If you're interested in lipids, the easiest way to
get started is to use CHARMM-GUI(, which will
give you both the coordinates and corresponding PDB, PSF and parameter

Jeffrey J. Potoff               
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815

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