Generate PSF structure

From: Peter Spijker (
Date: Mon Mar 08 2004 - 12:01:28 CST

Hi all!

For already a couple of weeks I am trying to create a PSF-structure file
from a PDB I created. But somehow, and I do not see why, it is failing
everytime. The structure I have is a lipid bilayer (DPPC molecules) with
explicit water as solvent and in the membrane a protein is embedded (the
B-2-adrenergic receptor). I am using the top_all27_prot_lipid.inp (and the
associated par_all27_prot_lipid.inp) to create the PSF file. I wrote a
simple Tcl-script according to the BPTI-example in the NAMD manual, but I
somehow cannot create the PSF structure file. If somebody can help me, that
would be terrific! If you want to give it a try, you can find the PDB-file
on: I did not include
the file so your mailbox would not explode. Thanks for helping.

Kind regards,


Peter Spijker, B.Sc.
Fulbright Fellow - The Netherland-America Foundation
California Institute of Technology
Biochemistry & Molecular Biophysics
Materials Process and Simulation Center
MC 139-74 Caltech
Pasadena, CA-91125
The United States of America
Phone: (626)-395-2844

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