VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 17 2011 - 11:28:24 CDT

Ignacio,
  Can you provide us with example files that don't load correctly with
the existing Molden plugin? If you can upload them to the VMD Public
project on BioCoRE, or post a .tar.gz file containing them on the web
somewhere, I would love to get these files and adapt the plugin to handle
the cases that it doesn't currently cope with. We wrote the Molden plugin
based on reading descriptions of the format, but having more example files
is very helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 17, 2011 at 09:12:33AM -0700, Ignacio Fernández Galván wrote:
> I've downloaded and installed the new VMD 1.9, hoping that it would finally
> allow me to view my Molden (QM orbitals) files. However, I still can't use it,
> because some keywords/features are not properly recognized. I understand this is
> probably not a prioritary of VMD, but I'll write here some of the issues:
>
>
> - Molden itself recognizes "(AU)" as a valid label for atomic units, while VMD
> expects it without parentheses. The code in Molden just searchs for the strings
> "AU" or "Angs". The problem is Molcas writes "(AU)", probably due to a
> misunderstanding of the format specification, but if it works with Molden, it
> should work with VMD.
>
> - VMD rejects a file with spherical d functions ([5D]). That's in itself a pity,
> and I hope the limitation will be lifted in the future. But: (a) It could load
> the molecule geometry, instead of just aborting; and (b) I does not similarly
> recognize [5D7F] or [5D10F], and maybe other keywords.
>
> - Anyway, in all my tests VMD complains about "Bad format in [GTO] section",
> even when I create the file by saving from Molden itself (so I'm pretty sure the
> format is correct).
>
> I hope this helps in creating a better molden plugin. I tried modifying the old
> plugin, but couldn't get it to work properly...
>
> Ignacio
>
>
> 

-- 
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