VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 13 2013 - 13:28:15 CDT

Hi,
  Can you gzip your .psf file and email it to me?
I want to see what file format you get when you used autopsf etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 13, 2013 at 03:25:44PM -0300, Alexandre Suman de Araujo wrote:
> Ops. Sorry.
>
> 1.9.2a14 version.
>
> Cheers
>
> --
> Prof. Dr. Alexandre Suman de Araujo
> Departamento de Física
> Instituto de Biociências, Letras e Ciências Exatas - IBILCE
> Universidade Estadual Paulista
> e-mail: asaraujo_at_ibilce.unesp.br
> 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
> > vmd_at_ks.uiuc.edu
> >
> >
> >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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/