VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 31 2006 - 17:57:18 CDT

This is correct..
The 'writing' feature of the psf plugin was implemented to help users
of SITUS who use PSF files for flexible fitting runs, where the PSF file
is (ab)used for purposes it wasn't really intended to serve. I have begun
extending the plugin interface in VMD to read and store the other data
one finds in a PSF file, but it's hard to say if I'll ever go so far as
to store everything that a PSF contains, or at least to store it in such
a way that you'd be able to do what you're attempting to do. If enough people
want to be able to do that, I'll consider it, but psfgen is surely the
better long-term way of doing these sorts of transformations on PSF files.
Perhaps we need to write a wrapper script for psfgen that does
the operation that you're attempting with an interface as simple
as what one can do with atom selections.

  John

On Thu, Aug 31, 2006 at 06:51:43PM -0400, Axel Kohlmeyer wrote:
> On 8/31/06, Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar> wrote:
> >Please help me because I am surely doing something wrong. I am using VMD
> >1.8.4 under Linux.
> >I load a both psf and pdb files from the shell for a protein in a water
> >box.
> >
> >$ vmd protein.psf protein.pdb
> >
> >I want to remove all the water so now from the tk console I put
> >set prot [atomselect top protein]
> >
> >$prot writepsf prot.psf
> >$prot writepdb prot.pdb
> >
> >Now if I take a look the psf from the shell
> >$ grep angles protein.psf
> >66246 !NTHETA: angles
> >$ grep angles prot.psf
> >0 !NTHETA: angles
> >
> >
> >So, the angles have magically disapeared. The same happens to the
> >dihedrals and impropers.
> >Is this a bug or are there some steps that I am missing?
>
> cesar,
>
> this is a 'feature': the psf reader in VMD does not read
> and store the information as it is irrelevant for visualization,
> only the bond information is read.
>
> my guess is, that you might get some help from the
> autopsf tool for what you want.
>
> cheers,
> axel.
>
> >
> >Regards
> >Cesar
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078