> I used openbabel to do this. It worked mostly fine but with a few compounds, 
> specially with the ones have protonated Nitrogen, gets destroyed.

What exactly do you mean by "gets destroyed?" Being more specific, or ideally 
providing a file and/or graphic would be very helpful.

Best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/
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