From: Alexandre Suman de Araujo (
Date: Thu Jun 13 2013 - 13:25:44 CDT

Ops. Sorry.

1.9.2a14 version.


Prof. Dr. Alexandre Suman de Araujo
Departamento de Física
Instituto de Biociências, Letras e Ciências Exatas - IBILCE
Universidade Estadual Paulista
Phone: +55 (17) 3221-2566/3221-2240
On 13-06-2013 15:12, John Stone wrote:
> Hi,
>    Which version of VMD are you using?
> Cheers,
>    John Stone
> On Thu, Jun 13, 2013 at 02:57:30PM -0300, Alexandre Suman de Araujo wrote:
>> 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