Opening ORCA output with Avogadro2

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I’m having issues in opening the Orca output files with Avogadro2. When I try to open the file, I get this error message:

Error while reading file ‘CH3CN.out’: Error while reading OpenBabel-generated CML: Error parsing XML: Start-end tags mismatch

I don’t have this problem with the old version of Avogadro on Windows, I tried to install it on Ubuntu 20.04, but I wasn’t successful (I had lot of troubles installing an old version of Qt, eventually I gave up). My OpenBabel version is 3.1.0.

Is there any solution to this incompatibility?

Thank you in advance!!

Cheers

2

Can you post the file (e.g., through a link with Pastebin, dropbox, google drive, etc.)? I’d need to see how the file is translated myself.

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Hi!

Thank you for your rapid response. You can find an output file on this link https://drive.google.com/file/d/1k_DOHl1RhY1DOxBRtb7eQYnG4snVr8re/view?usp=sharing
This is read without problems by the old Avogadro, that shows the MOs, the structure and so on. Avogadro2 can’t even open it. Any help will be much appreciated!!

Cheers

4

It opens okay for me - what beta of Avo2 are you using?

You mention that you have Open Babel v3.1.0 - can you confirm that obabel CH3NO2*.out -ocml works?

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Hi!

I’m using the 1.93.0 version (the latest release I guess). Actually the command you told to try doesn’t work, it gives the following output:

obabel: cannot write output file!
Open Babel 3.1.0 – Jun 3 2020 – 18:27:23
[…]

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How did you install Open Babel?

If you run obabel -L cml do you get some help text about CML? (I would guess no.)

It seems as if this version doesn’t have CML support… I’ll have to see what we can do for that.

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Yes I confirm that “cml is not a recognized plugin type”. I installed OpenBabel following the guide on the official site, here: https://openbabel.org/docs/dev/Installation/install.html

Can I install the plugin somehow?

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Dear ghutchis,

I partially solved the problem by reinstalling OpenBabel. Now I can open the output file and the molecule is shown, but I don’t see the molecular orbitals, and there seems to be no option to do so. Is there any plugin I can download or am I missing something? Thank you!

Best
Giuseppe

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10

Hmm. I’ll need to check what’s going on more carefully. We may need a new Orca reader in Avogadro2.

In the meantime, you should be able to use a molden file:

orca_2mkl file -molden

I’d like to get MKL support in place - I’ve found that gzip / bzip2 MKL files are actually smaller than the original .gbw file from Orca, and you can re-generate the .gbw file like this:

bunzip2 file.mkl.bz2
orca_2mkl file.mkl -gbw
# now file.gbw exists to restart
11

Since this thread is coming up often in Google search results, I’ll mention that the latest releases of Avogadro2 include a native ORCA reader including depicting orbitals, etc.

We do not yet support the MKL format, mostly because Molden and other formats are more widely used.

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