Dear all
I am trying to saturate molecules in .xyz files with hydrogen according to the valence of the atoms in the file using openbabel. I'm not sure if I understand how it does the hydrogen saturation however, as I'm not getting the behaviour I expected. For the input file "fragment.xyz" which looks like, 1 C 0. 0. 0. I execute the command, obabel fragment.xyz -O fragment_H.xyz -h expecting "fragment_H.xyz" to contain the coordinates of three hydrogen atoms. Instead, I get, 1 fragment.xyz C 0.00000 0.00000 0.00000 Is it possible to get openbabel to add hydrogens to saturate valence? Puck van Gerwen Doktorandin / PhD candidate Departement Chemie Klingelbergstrasse 80 CH-4056 Basel https://www.chemie1.unibas.ch/~anatole/index.html
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