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.
In this case, I’d suggest you use Open Babel (the conformer generator) directly.
obabel initial-file.cml -O conformers.xyz --conformer --nconf 20 --weighted --writeconformers
Great, thank you so much!
@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.
Never mind. I was accidentally using an older version of OpenBabel (there are so many versions floating around out there).