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Avogadro 1.93.0 Export Molecule does not work

Dear all,

I am using Avogadro 1.93.0 and I am facing a problem when trying to export molecular structures in xyz data format (or any other data format available at “Export Molecule…”). Error message: “Unable to find suitable file writer for the selected format”. I am running Avogadro at Ubuntu 20.04 and Qt version 5.12.8. There is a workaround using the “Build -> Atomic Coordinate Editor” and then copy the coordinates into a new file. However, does anyone know how to fix this issue?

Many thanks and best wishes,
Urwald

Saving to XYZ should happen from internal code, so I’m not sure why that’s happening. How did you install Avogadro, and what version of Open Babel are you using?

Hi ghutchis,

I installed Avogadro via the package manager (apt-get install avogadro). I am using openbabel v.3.0.0 (also installed via package manager).

Best,
Urwald

When you go to Export as an XYZ file do you see this dialog?

Obviously, you’ll want the Avogadro option.

I am getting a different dialog than youavogadro_error

Edit: Just to be absolutely sure, I am talking about the new Avogadro2 (v.1.93.0)

And just to be sure, you set the extension to ‘.xyz’ right? What was the filename?

As I said, I could understand if something is weird with obabel (e.g., it’s not in your path) but there’s native code for writing XYZ files.

Let me see if I can get an Ubuntu package built from Github.

Ok, mistery solved. I just did not add “.xyz” to the filename, because I chose “XYZ” from the file type pull down menu. After adding .xyz everything works as intended. Sorry for wasting your time and thank you.

Interesting!! I happened to have similar problem. I am following the gromacs tutorial:

Open jz4.pdb in Avogadro, and from the “Build” menu, choose “Add Hydrogens.” Avogadro will build all of the H atoms onto the JZ4 ligand. Save a .mol2 file (File -> Save As… and choose Sybyl Mol2 from the drop-down menu) named “jz4.mol2.”

url : http://www.mdtutorials.com/gmx/complex/02_topology.html
But there is no drop-down menu.
I install Openbable and Avogadro using apt-get install.

Yes, that tutorial is using Avogadro v1. You can get the same result from Avo2 (1.93) using Export => Molecule.

We’re of two minds about separating out the “export” from the “Save As” command. A lot of users don’t realize they lose data when they save to XYZ or PDB - and then complain the ‘bonds are wrong’ when reading back. So we separated out the native formats for “Save As…” and other formats for Export.

No, it’s still helpful - it should be adding the extension when you specifically pick a format. I’ll go check that.

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