VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 29 2011 - 10:23:49 CDT

Ignacio,
  I was playing with the files you've already sent and the examples
you provided are all using the 5D spherical basis that isn't yet supported.
Do you have any test cases that give you the "Bad format in [GTO] section"
error message that are not using a spherical basis? I just changed the code
to recognize the "(AU)" string emitted by Molcas, so that much should be
fixed/improved already.

Thanks,
  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
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