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Compilation of avogadro-1.2.0 on Ubuntu 20.04 LTS

I tried installing Avoagdro from apt on ubuntu 20.04 LTS. This seems to have worked, though I apparently installed avogadro2 and not the “old” avogadro. After also installing openbabel I could “optimize” the structures, however using GAFF, hydrogen atoms get mangled and I miss the “interactive” energy minimization mode.

I tried to download the the avogadro-1.2.0 source from the website and compile. This turned out to be related to some issues. First, running cmake …/ I was alerted to the fact that I needed qt4 and qt5 is now the default apt available version.

I managed to install qt4 though repeating cmake …/ I was now alerted to the fact that I did not have openbabel 2.x installed which is correct as apt installs version 3.

I suppose my questions are these, is there a way around having to install qt4 specifically? qtchooser seems to indicate that I have 4, qt4-x86_64-linux-gnu and qt4 installed. I guess these came bundled with qt5-default(?). cmake obviously caught qt5 as the installed version, I am now curious as the name (qtchooser) seems to indicate it being possible to select a version for use. Is it possible to couple this with cmake or is it only for qmake?

Is there a way around using openbabel2?

And finally, which should likely have been my first question, is there a way to use the “interactive/live” energy minimization mode in avogadro2?

All the best
// Gustaf

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No. Avogadro 1.x was written with Qt4, and there’s little interest on my part to port to Qt5. I’d rather spend the time finishing up Avo2.

Is there a way around using openbabel2?

Again, no. In particular, Avo 1.x was written to directly integrate with Open Babel 2.x. It made development much easier, but porting to OB3 would take a lot of work.

And finally, which should likely have been my first question, is there a way to use the “interactive/live” energy minimization mode in avogadro2?

At the moment, no, because work on the integrated force field implementation is not yet done. Now that the semester is over, it will be easier but I’d expect “mid-to-late-summer.”

I do know many people who use Avogadro 1.2 through a Windows layer on Ubuntu.

Certainly we’re working to finish Avo2 sooner rather than later and promise the result will be worth the wait.

The features I’m missing are then bound to become available at some point. I’ll start working with Avogadro2 and get used to the new interphase, that will likely make things feel more comfortable.

Thank you for the clear replies, making the software available and all the hard work.

Best regards
// Gustaf

The Avo2 interface is still somewhat in flux. I suspect we’ll have at least one more menu reorganization.

That said, everyone should absolutely provide feedback about what they do and do not like about Avogadro 2.

We (mostly @mhanwell) rewrote the engine. Now it’s about making everything fly smoothly. :slight_smile:

Lots of plans…

Thanks to the developers for the wonderful piece of software.

I had few questions regarding the Avogadro2 version that is now available from the repository for Ubuntu 20.04.

  1. Would it support analyzing ORCA outputs natively? I know that Avogadro 1. x does that natively. This feature would be really nice to have.

  2. The last time I had checked Avogadro2 on Ubuntu 20.04, I observed that we cannot export files in PDB format. It would ask for the name of the file, and then reopen the window again without saving the file.

Best,
Hemanth

Yes, Avogadro reads Orca output files, either through Open Babel or cclib.

This was, not surprisingly, a bug. It was fixed months ago.

Thank you for the clarifications.

Best Regards,
Hemanth