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Showing multiple results from conformational search


#1

I am using version 1.2.0 (Windows) version of Avogadro. Is there any way to display or save (e.g. as .xyz file) the best N results from a conformational search instead of just the lowest energy structure? Ideally I would like to search for many conformers and take the lowest (let’s say) 10 to optimize further with DFT.


#2

In this case, I’d suggest you use Open Babel (the conformer generator) directly.

https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#generating-conformers-for-structures

e.g.

obabel initial-file.cml -O conformers.xyz --conformer --nconf 20 --weighted --writeconformers


#3

Great, thank you so much!


#4

@ghutchis. Unfortunately I never got around to testing this, but now I have and it seems only the final conformer is generated unless I use the default genetic algorithm. Any idea why this would be? To clarify, doing obabel.exe test.sdf -O conformers.xyz --conformer --nconf 20 --weighted --writeconformers --ff UFF saves 1 conformer in an XYZ file whereas obabel.exe test.sdf -O conformers.xyz --conformer --nconf 20 --writeconformers --ff UFF saves 20 in the XYZ file.


#5

Never mind. I was accidentally using an older version of OpenBabel (there are so many versions floating around out there).