VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 13 2013 - 13:12:44 CDT
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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/
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