From: Axel Kohlmeyer (
Date: Mon Jun 21 2010 - 17:25:22 CDT

On Mon, 2010-06-21 at 17:41 -0400, Lai zaizhi wrote:
> On Mon, Jun 21, 2010 at 3:56 PM, Lai zaizhi <>
> wrote:
> Hi,
> I have the amber topology file .prmtop and .pdb file, now I
> want to convert them to .psf file using vmd. What should I do?
> I found some archieves, yet they don't include more details,
> and I also check the manual of psfgen. It seems like psfgen
> has no command to convert prmtop to psf. Any suggestions will
> be very welcome! thanks!

on the vmd command line type:

mol new myfile.prmtop waitfor all
animate write psf myfile.psf waitfor all

please note, that this will strip off
a lot of additional information that is
contained in the .prmtop file that a .psf
file does not contain.


> Good day!
> zaizhi lai

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.