It is printed on stderr , so 2> is the appropriate syntax for a shell type call.

Or you can use Capture::Tiny to capture all output 
http://search.cpan.org/~dagolden/Capture-Tiny-0.46/lib/Capture/Tiny.pm


> On Oct 2, 2017, at 11:36 AM, Jose Gascon <joseagas...@gmail.com> wrote:
> 
> Greetings
> 
> I have a perl script that calls obabel to convert the format of a
> structure. The conversion always prints to the screen "1 molecule
> converted". Is there any way to suppress that message? Directing to
> some sort of a log file via ">" does not work.
> 
> Thanks in advance,
> 
> Jose
> 
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