From: Θωμας Ευαγγελιδης (
Date: Fri Sep 21 2007 - 06:12:49 CDT


you need to use psfgen plugin. First download the topology files from:

Read psfgen's manual, there's a comprehensive example there (if your pdb
contains only waters, ignore the protein part in the example).
There’s a known problem with psfgen and water representation in VMD. By default
the waters will seem like triangles
( ). You can
change that by replacing this line in your topology file :

BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake

By this one:

BOND OH2 H1 OH2 H2 ! the last bond is needed for shake

But I think that if you want to use your .psf for simulations, you must not
modify the topology file.

Good luck,
Thomas Evangelidis

> Dear all,
> I am trying to generate a PSF file from a PDB which contains water
> molecules. I used AutoPSF VMD plugin but it did not work. I tried
> using "pdbalias residue HOH TIP3" in a file but it did not work as well.
> Do you have any suggestions?
> Andrea Cristiani
> LCT-Biochimie Pharmaceutique
> Universitι de Genθve