From: Alexandre Suman de Araujo (
Date: Thu Jun 13 2013 - 12:57:30 CDT

Hi all

I have a .psf file generated with CGenFF topology file and "Automatic
PSF Builder" plugin from VMD. The obtained .psf file has atoms with
atomtype field with different sizes, ranging from 4 to 6 characters, as
expected. I use this .psf and the obtained .pdb in NAMD simulations with
CGenFF force field parameter files without problems.

If I load this .psf and .pdb in VMD, open tkconsole, build a selection
with all atoms and use the writepsf command I obtain a new .psf where
all atomtype fields has the same size: 4 characters. The last characters
are lost and this .psf is broken, since the atomtypes of this .psf do
not match anymore with the ones in the CGenFF parameters file.

Is this a known limitation in writepsf routine or there is some way I
can use it (with some option) where it writes the atomtypes correctly?

Best regards

Alexandre Suman de Araujo