> I am facing a similar problem. I dowload ligands in sdf format from pdb
> website.

Can you give us particular examples? Particular links? Particular problems? 
What version of Open Babel are you using? What OS?

Right now, I'd say "it works for me" because I've processed the entire 
LigandExpo from the PDB website with no problems.

Thanks,
-Geoff
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