Avogadro2 - I do not see openbabel conformer search results

Miroslav_Ilias · July 5, 2025, 11:11am

Hello,

on my WSL (Ubuntu22.04) I installed most recent ./Avogadro2-x86_64.AppImage .

I loaded molecule (benzene-1,2-diol) for conformational search.

While with the CREST extension I can reach conformers search results (~/.local/share/easyxtb/calcs/last), I can not reach them using Open Babel.

Please where can I see Open Babel - in - Avogadro2 results ?

ghutchis · July 5, 2025, 11:32am

Open Babel uses a rule-based conformer search. It does not consider -OH bonds for analysis because at room temperature they randomize.

If you want to compare the different conformers of benzene-1,2-diol.. yes you’ll need to use CREST - or take the conformers from CREST and calculate energies with the Open Babel force fields.

Miroslav_Ilias · July 5, 2025, 1:01pm

But indeed, this time I took tartaric acid.

Avogadro 1 shows conformes from openbabel , they are visible via View-Properties-Conformer Properties.

But Avogadro2 does not show them …I know where to find CREST results, but where to find openbabel conformer search results please ?

In Avogadro 2 (which I have under WSL) the Conformer Properties (under Analyze - Properties - Conformer Properties) is not active…maybe something wrong with the installation ?

ghutchis · July 5, 2025, 6:58pm

No, it looks like a bug. I tried a highly branched alkane which clearly should generate a bunch of conformers.

I’ll have a patch.

ghutchis · July 6, 2025, 4:22pm

Here’s the pull request - I’ll merge it later today:

github.com/OpenChemistry/avogadrolibs

Fix reading 3d sets from cjson

master ← ghutchis:fix-cjson-3dsets

opened 08:33PM - 05 Jul 25 UTC

ghutchis

+100 -20

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Miroslav_Ilias · April 3, 2026, 5:18am

Hello again,

almost year has passed and I am again checking conformers search with the fresh Avogadro 2.0.0 under MS Windows 11.

This is my testing molecule tripeptide_UFF.cjson (4.3 KB) but again, after running Extensions-OpenBabel - Conformer Search I can not find any conformer results.

Please help.

matterhorn103 · April 3, 2026, 2:50pm

Are you still using the Linux AppImage under WSL or is this issue occurring with the Windows binary?

ghutchis · April 3, 2026, 5:15pm

Open Babel does not consider terminal methyl groups as rotatable. I don’t know about the valine side-chain bond, but this is not the best case study for “are conformer searches working.”

I looked at iso-octane and while it’s performing the search (i.e., the geometry changes) I’m not seeing conformer properties.

Helium5793 · April 5, 2026, 12:24pm

I too am having problems with this. I chose arachadonic acid as a test case. Ran it through according to the tutorial (same settings). When I got to conformer properties it was grayed out. I first tried it on my fedora linux system (version 1.103.0) and then on a windows 10 system (2.0.0) with the same result.