VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 09 2004 - 10:00:14 CDT

Ara,
  Looks like the PSF file you're using is formatted incorrectly.
Also, what are the units that your atom coordinates were specified
in in the XYZ file? A quick examination leads me to believe that they
were specified in nanometers rather than angstroms, which is why VMD
gets upset when you try to load the XYZ file by itself. If you scale
the atom coordinates by 10, you should get better results even with just
the XYZ file. What program did you use to write the PSF file? The PSF file
is definitely not formatted in the normal way, so VMD is not parsing it
correctly. Surprisingly enough it continued reading it anyway.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 09, 2004 at 08:49:16AM -0600, Kooser, Ara S wrote:
> John,
>
> Thank you very much for your help. I noticed when I am in VMD and I go to
> the graphical representation and choose selection. My atoms are not typed
> correctly.
> Currently I just have the gold surface by itself. Our lab is being
> overhauled so I can't get to the surface with waters. The gold surface .psf
> and .xyz are attached to this e-mail. Thanks again.
>
> Ara Kooser 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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