VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 24 2008 - 15:46:14 CDT

Hi,
  If you're running VMD on MacOS X, it's just as easy to simply run
VMD the normal way and use these commands to do the same thing:
  cd /path/to/the/directory/where/ubq.pgn/is/
  play ubq.pgn

Make sure you were in the right directory when you ran the ubq.pgn script.
If you still have problems after that, let us see the contents of your
ubq.pgn script.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 24, 2008 at 02:24:16AM -0500, Montoya, Jesus Gerardo Galaz wrote:
> I've been having problems to make "vmd -dispdev text -e ubq.pgn" work while working on one of the NAMD Tutorials. (I'm using a MacOsX Leopard).
>
> When typing on a VMD terminal:
>
> vmd> /Applications/VMD\ <version>.app/Contents/vmd/vmd_MACOSX
> dispdev text -e ubq.pgn
>
> as suggested in the tutorial, all I get is:
>
> invalid command name "/Applications/VMD <version>.app/Contents/vmd/vmd_MACOSX"
>
> I checked the contents of the VMD 1.8.6 package and the file at the end of the pathway seems to be vmd_MACOSXX86 instead of vmd_MACOSX, yet I got the same result at the terminal when typing:
> vmd> /Applications/VMD\ <version>.app/Contents/vmd/vmd_MACOSXX86
>
> After reading some of the messages on this VMD list I also tried:
>
> vmd > play ubq.pgn
>
> But got the following back:
>
> 1.4.5
> too many arguments specified
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> invalid command name "pdb ubqp.pdb"
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> etc...
> And I was using the '.pgn' file generated with the lines in it exactly as indicated in the tutorial (in fact, I just did a 'copy-paste' from the tutorial .PDF file to a blank document on Nedit which I saved as 'ubq.pgn').
>
> What should I do??
> Thanks!
> Jesus 

-- 
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