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

From: Ranyere Deyler (
Date: Mon May 17 2010 - 16:57:10 CDT

Hi. Well, depending on your system, you can generate bonds, angles,
dihedrals and impropers from topotool plugin 1.1 of VMD. I don't know the
accuracy of the impropers, but when i used it for bonds, angles and
dihedrals it worked just fine.

just download the latest plugin of topotools, version 1.1, and do something
like that:

package require topotools 1.1
topo retypebonds
topo guessangles
topo guessdihedrals
topo guessimpropers
set sel [atomselection top all]
$sel writepdb file.pdb
$sel writepsf file.psf

But the proble is, if you're gonna run it on NAMD, you'll need the
ForceFields parameters of angles, dihedrals and impropers, and it may be
hard to be found if you're dealing with an unusual system.

On Sun, May 16, 2010 at 3:35 AM, Jeffrey Potoff <
> wrote:

> 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 files.
> --
> ======================================================================
> 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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