VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Aug 31 2006 - 17:51:43 CDT

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.