I am using Avogadro2 to generate an input file for phenyllithium.
If I start with benzene, I can change one H to Li using the draw tool, but the Li is in exactly the same place the H was, so if I used that geometry the C-Li starting bond length would be much too short. So I tried the “optimize geometry” feature in Avogadro2…but it does nothing. None of the atoms move.
–David Shobe
Can you please provide a bit more information?
What version of Avogadro2 are you using?
What OS are you using?
Have you tried a nightly build from https://two.avogadro.cc/
etc.
More information, as requested by @ghutchis:
Avogadro2: 1.99.0
OS: Windows 11
What’s a nightly build? Is it an auto-update system? Anyway, I have not used it.
I did try unfreezing all atoms, so it wasn’t that.
I have not specified a particular force field or anything like that to use. Could that be the problem?
–David
I’m really suspecting the force field, because optimize geometry does work for hydrocarbons. Is there any way I can get it to use a force field that includes more elements? Even a simple one using average atomic radii and VSEPR theory would be better than nothing.
–David
Nightly builds are exactly what they sound - built every night from the latest code (i.e., development, not release). Since we do fix bugs continuously, it may address your problem.
There should be several force fields available, including MMFF94 and UFF. I would suggest looking under Extensions ⇒ Calculate ⇒Configure… to see what’s available for a particular molecule.
What happens if ORCA is running during the nightly update?
I looked under Extensions => Calculate => Configure and I was using UFF by default. The only other option was LJ, which crumples up the molecule into something unrecognizable. Out of curiosity, I changed it back to UFF and reoptimized, and am pleased by the result. The two step optimization with two different force fields worked!
–David
A local instance of ORCA won’t affect your nightly build, if I remember correctly you have to redownload the nightly build to get it to update the application.
There are a few kinks in the force field optimization parts of A2, but in general either restarting the program or just reselecting options makes things work.
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