- Don’t use Avogadro 1.2, it’s very old. You should get a recent release, ideally a nightly build – see Install — Avogadro 1.99.0 documentation
- Avogadro isn’t currently able to start calculations with ORCA for you, you will have to do that yourself. What it can do is prepare an ORCA input file for you – see for example this recent thread – for which you’ll need to make sure Python is set up and working properly on your system.
- In general to set the overall charge on your Avogadro molecules you will need a recent nightly build, and then it can be set under Analysis > Properties > Molecular.
Personally I always found it easier to use Avogadro to create an input geometry and then write the ORCA input file manually in a text editor, as the ORCA syntax is pretty simple, the manual is very helpful, and you then have full control.
So I typically just sketch a molecule by hand, do a quick pre-optimization in Avogadro with the built-in force fields or with xtb, then export it in XYZ format, and simply refer to the XYZ file in the coordinates block of the ORCA input file.
Again, if doing pre-optimization in Avogadro then you’ll want to make sure the overall charge on your ions is set appropriately to ensure that the results make sense.