Can Avogadro open an output from Gaussian?

General Discussion
1

Hello, I recently ran a geometry optimization in Gaussian (09) for a large molecule (99 atoms), and now I would like to convert the coordinates of the optimized geometry from the Gaussian output file to a pdb. Is Avogadro capable of reading the coordinates section of a Gaussian output file? Thanks!

2

Of course, no problem.

3

Great! How does it work? I have tried opening the entire output file (which is quite large and consists of multiple geometries), and it failed. I also tried copying just the coordinates of the final geometry and making a new text file saved as .log, but this also did not open.

4

I have tried opening the entire output file … and it failed.

Can you be a bit more specific? Avogadro can read output files directly.

I also tried copying just the coordinates of the final geometry

You can paste this into the Cartesian Editor as well. In Avogadro 1.2, it’s under Build => Cartesian Editor. In Avogadro 1.9x it’s under Build => Atomic Coordinate Editor.

You’ll need to tweak the format once you paste, since Gaussian includes the atom index in the first column and charges (usually 0) in the 3rd column.

5

For the output file that failed, I just tried opening the entire output file from Gaussian: a 5 MB text file containing optimization data for each iteration in addition to the final coordinates. I figured that it would not open or know how to recognize the coordinates.

The editor worked well, however. Thank you for your help!

6

Can you tell me what exactly happened when you tried to open the output file? It reads Gaussian output - and yes, finds the final coordinates.

So I’d like to know what “failed” mean - threw up an error? Didn’t show a molecule?

Can you share the file?

Thanks!

7

If I try to open the file, it says “reading multi-molecule file. This may take a while…” then a box pops up that says “Reading molecular file failed” then gives the path to the file. Looks like I can’t share the file… because it’s not an image? Is there an avogadro support e-mail I can send it to?

8

You can find my pitt e-mail address. :slight_smile:

Thanks!

9

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