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I believe this to be a bug with Avogadro:
(Please describe your bug or issue)
Environment Information
Avogadro version: 1.102.1
Operating system and version: windows 11
Expected Behavior
Hello,
I am following this webpage in an attempt to perform conformer search using open babel. However after performing the search the final conformer properties button is not available to click (see picture). Any advice?
The conformer search causes the active molecules to rotate and shift in shape, but it seems a library of conformers is not being created?
It would help a lot to know what conformer search you used. Some of them do not necessarily generate the full set.
I’d also suggest checking out the latest continuous build from Install — Avogadro 1.102.1 documentation - I definitely fixed a bug with conformers not being available, but I can’t remember whether that made it into 1.102.1 or not.
Hi, i also have the same issue with Avogadro 2.0. I tried the Windows normal and nightly builds, and also linux flatpak but OpenBabel conformer search just doesn’t work. In systematic search it always shows a number of “0 conformers” to search and with other searches it does nothing, sometimes it changes the geometry of the molecule (i did many tries with substituited cycloalkanes and butane), but the option Analyze → Properties → Conformer Properties is never avilable. For the mean time my Avogadro 1.2 Systematic Search works, and i’m looking forward to see if CREST plugin is a more atractive option
It depends on your needs. CREST is intended as an exhaustive tool to generate a low-energy ensemble. If you’re doing quantum chemistry and want Boltzmann-weighted conformers, then CREST is a great tool. (It can be slow though because it often runs both dynamics and hundreds of optimizations.)
If you want a geometrically-diverse ensemble, etc. then CREST is not so useful.
I’m not sure why this wouldn’t work for Windows, but on Linux, it’s definitely tied to the version of Open Babel installed. OB v.3.2 and later include full CJSON support and should supply the full ensemble.
On Windows, there should be an avogadro2.log file in your Documents directory. If you can upload that, I should be able to see why CJSON isn’t being used.
In the meantime, let me see if I can update some Python plugins to provide other options.
Ok thank you very much for the information. I’m using the conformer search to prepare structures for further quantum chemistry calculations (DFT with gaussian), maybe having the two tools (OB and CREST) would be interesting. Here is my avogadro2.log file, thanks again!
Given your use case, I’d probably suggest CREST, since it attempts to produce an exhaustive ensemble of Boltzmann-weighted conformers.
In the meantime, the latest RDKit and openconf plugins for Avogadro can now generate conformer ensembles as well. (I’m still trying to figure out why it’s not giving you all the conformers for an Open Babel search.)
