VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 20:47:40 CDT

Hi,
  The psfgen user's guide explains the "poorly guessed coordinate"
warnings. They are emitted when psfgen guesses coordinates for
atoms but the topology file doesn't contain lengths or angles them.
  http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 04, 2006 at 06:17:17PM -0400, Margaret Shun Cheung wrote:
> Dear VMD wizards,
>
> I tried to generate psf from a pdb structure. It gave me warning messages
> on N-, and C- residues when I run the script:
>
> Warning: poorly guessed coordinate for atom HT1 ....
> Warning: poorly guessed coordinate for atom HT2 ...
> Warning: poorly guessed coordinate for atom HT3 ..
> Warning: poorly guessed coordinate for atom OT1 ...
> Warning: poorly guessed coordinate for atom OT2 ..
>
> Can I ignore this warning? Thank you very much.
> Sincerely,
>
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

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