VMD-L Mailing List

From: Francesca Mocci (francy_at_mail.dsc.unica.it)
Date: Thu Sep 14 2006 - 09:26:43 CDT

Hi Jan,

thanx a lot for your prompt advice:

- either deleting in the g03 log file the column of "Atomic Type"
    which consist of 0s and then loading it as a gaussian94output
- either loading the unmodified g03 log file through the plugin QMtool
    found in the simulation submenu of the extension menu
the file is loaded correctly.

Francesca

Jan Saam ha scritto:

>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
>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>>
>>
>
>
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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    
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~