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!
Of course, no problem.
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.
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.
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!
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?
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?
You can find my pitt e-mail address.
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