VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Thu Sep 14 2006 - 08:09:09 CDT

Hi Francesca,

the format of Gaussian logfiles has changed between G98 and G03. (I
think another column containing zeros has been added to the table where
the coordinates are read from, you could delete that column manually and
it should work)

However a better solution is probably to load your file using the plugin
QMtool. It is able to read G03 files and makes use of more info than
just the coordinates. you'll find QMtool in the extensions menu.

Good luck,
Jan

Francesca Mocci wrote:
> Hi all,
>
> I'm using vmd.1.8.5 (linux) and I would like to visualize
> a gaussian 03 log file (containing several frames).
> In the "molecule file browser"
> I determined the file type as "Gaussian94output"
> and then I load it.
> Unfortunately the structures are visualized in 2 dimensions
> like the projection in a plane of the actual structure.
> I checked the log file with other visualisation program and it is fine,
> I can see the correct 3d structure.
> The problem is the same with all the g03 log file that i checked.
>
> Is there a way to fix this problem?
>
> Thanx in advance,
> Francesca
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Francesca Mocci,
> Dipartimento di Scienze Chimiche,
> Università di Cagliari
>
> Phone:+39 070 675 4362/4394
> Fax: +39 070 675 4388
> E-mail: francy_at_dsc.unica.it
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de