VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 15 2009 - 16:56:34 CDT

Hi,
  The warning you're getting is because the AMBER parm reader plugin
doesn't (yet) provide VMD with information on angles/dihedrals/impropers.
If you send me the files you're working with and tell me which version of
AMBER you're using, I can try and have a look at this next week when I
have more time available. In the mean time, you might try using
the AutoPSF GUI for this purpose and see what it can do for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 15, 2009 at 02:35:23PM -0700, Goutham wrote:
> Hey All,
> I am trying to generate a PSF file for a given amber input files. Using
> the top and crd files, I am able to load it in VMD. I tried making a
> selection of all atoms after that, and tried "writepsf". But this gave a
> warning:
>
> PSF file is incomplete, no angles, dihedrals, or impropers will be
> written.
>
> Can anyone help me if I can generate a proper psf file from here?
>
> Thanks
> Goutham 

-- 
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