[Open Babel] Adding Hydrogens

[Christopher Beeler]

Hello, I am currently trying to use OpenBabel to add hydrogen to my XYZ molecules but it is not adding any. I am using version 2.3.2 on Linux. I have attached the input and output files. The command I am using is 'babel -ixyz molecule_1.xyz -oxyz molecule_1.in -h'. The output file should have 8 hydrogen now but it still contains 0.


Thank you-Chris Beeler, ***@dal.ca

[Noel O'Boyle]

"-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
valencies, but rather converrts implicit to explicit hydrogens. You
can open in Avogadro and click "Build/AddHydrogens" to do this.

Could I ask you where the XYZ file came from? It may be that a
different route might help.

Note to Geoff: would this be a useful 'op' or else option on XYZ?

- Noel

Post by Christopher Beeler
Hello, I am currently trying to use OpenBabel to add hydrogen to my XYZ
molecules but it is not adding any. I am using version 2.3.2 on Linux. I
have attached the input and output files. The command I am using is 'babel
-ixyz molecule_1.xyz -oxyz molecule_1.in -h'. The output file should have 8
hydrogen now but it still contains 0.
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[Geoffrey Hutchison]

Post by Noel O'Boyle
"-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
valencies, but rather converrts implicit to explicit hydrogens. You
can open in Avogadro and click "Build/AddHydrogens" to do this.

Well, Avogadro will just call Open Babel. ;-)

Post by Noel O'Boyle
Note to Geoff: would this be a useful 'op' or else option on XYZ?

Maybe? It's probably more useful as an 'op' because there may be other files that come in with "missing hydrogens"

-G