Geometry optimization and coordinate manipulation in Avogadro 2 v1.97.0

General Discussion
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Hello, I need to accomplish two things in Avogadro 2 (v.1.97.0 running on Windows 11) that I accomplished using Avogadro:

  1. Optimize geometry (“molecular mechanics” is not available in Extensions)
  2. Translate coordinates (I need to rotate my molecule 90 degrees)

I’m not finding these features in Avogadro 2. Also, I did not find a user guide/manual for Avogadro 2 on the landing page (Install — Avogadro 1.97.0 documentation)

Kind regards,
Sean

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Though my observations are for the Linux AppImage, I assume the GUI for the Windows executable is the same there.

Extensions → OpenBabel → Optimize Geometry, or the short cut by Ctrl + Alt + o offers an optimization. Noteworthy is Extensions → OpenBabel → Configure Force Field for that one can elect one of multiple force fields (GAFF, or Ghemical, or MMFF94, MMFF94s, or UFF) how the optimization should proceed and exit early provided adjustable criteria are met.

I don’t recall if there once was a coordinate transformation menu in Avogadro to either translate, or rotate a molecule. Wouldn’t this matter as relative orientation in presence of at least one other molecule in the same model? Or do you want to rotate e.g., a trifluoromethyl group around the sigma bond of C (of the CF3 group) to C (of the molecular frame the CF3 group is attached to)?

3

Thomas,

Thanks for your reply. I didn’t get a notification for some reason. Yes, thank you for steering me to the optimize geometry function. Seems to work fine.

For the coordinate transformation, I need to align the axis of an ethylene unit with the z-axis because I’m in turn using the coordinates as input for moltemplate to build a larger system. I suppose the system is simple enough that I could just enter the coordinates manually, but for a more complicated system that would be a pain.

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@sean

Hello Sean,

sorry for the delay, I hope this time the message reaches you promptly.

I wasn’t yet aware about moltemplate - I assume it is the project you refer to. However, with some of the illustrations from this repository in hand, and your description, the reasoning is evident.

For now, I identified orient-molecule as a handy implementation which can translate and rotate/reorient the molecules. Based on a test with an openbabel generated model of diethyl ether, the Python based utility (padded by numpy) seems to work e.g., by

python3 ./orient.py -rz 90 ./diethylether.xyz > rz90.xyz

The simultaneous display of both the original as well as the modified model file by Jmol yields this:

example

The attached markdown log describes the individual steps. Right now, I do not recall if openbabel’s documentation includes a diagram about the coordinate system’s handiness. Do you know if there is a convention?

log.md.txt (1.4 KB)

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Thomas,

I apologize for the delay. This time, it was my fault. Thank you very much for this solution, it is much appreciated! This would be a useful feature to add to the GUI. I can bring it to the attention of the powers that be.

Regarding the coordinate system’s handiness, I do not know… when I link to this post with the feature request I can include that question.

Better yet, I can just @ghutchis.

Thanks again!

Kind regards,
Sean

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