Optimize geometry giving error

General Discussion Support
#1

I believe this to be a bug with Avogadro

Avogadro2 1.91.0
MacBook Air
MacOS sierra version 10.12.6

Optimize geometry giving error

Error interpreting Babel MDL output.

#2

That version seemed to be a bad build.

For now, you might try this build of 1.93 / latest for Mac:
https://github.com/OpenChemistry/avogadrolibs/suites/637580336/artifacts/5283787

#3

loaded 1.93.0 mac and i still having the same problem.
I can also try PC version later.

#4

Hmm - you sent me some of your files, so I’ll take a further look.

#5

thank you number 2 is the file i am trouble with

#6

I’ve figured out the issue - it’s really big. I don’t have any quick answers inside Avogadro.

  1. You can run obabel yourself to minimize. If you have Open Babel installed (e.g., via homebrew), you can run:

obabel ~/Desktop/geoffclark/geoff-clark-2.cml -O optimized.cml --minimize --ff uff
#warning this can be slow

  1. Another thing I’d suggest is to install xtb using Anaconda (https://docs.anaconda.com/anaconda/install/mac-os/)

    If you have conda installed, you can use conda install -c conda-forge xtb

    Then save your systems as XYZ files and run:

    xtb geoff-clark-2.xyz --opt | tee xtb-opt.log

This particular file is 2700 atoms, so it will be slow.

I’m working on an integrated force field engine in Avogadro2, which would make it possible to run xtb and other programs interactively, but it will be a few weeks.

#7

And by slow, I mean hours even with obabel. One advantage of xtb is that it will use all your cores, but I’d still guess many hours to optimize.

#8

Thank you, i will install these and give them a try.