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.

9

when will Geometry optimization be working on avogadro 2 for the mac?

10

A post was split to a new topic: Images for a Whole Directory

11

Try one of the latest nightly builds from https://two.Avogadro.cc it works great on my Mac…

12

Avogadro 2 working great on the Mac, Thank You
question, when i have two molecules on the screen and i select one with the selection tool.
then i want to use the qwerty keys to manipulate and rotate it, the keys rotate both molecules like it was the navigation tool are there qwerty keys to manipulate just the molecule I selected ?

13

Yes, at the moment, the manipulator tool does not support the qwerty / arrow keys and so it will just pass that to the navigation features.

I’m in the middle of finishing grades, but I want to add the manual manipulation features (including keys) this week. I’ll update the thread when there’s a build to test.