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PostPosted: Wed Feb 26, 2014 9:33 pm 
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Joined: Wed Feb 26, 2014 9:07 pm
Posts: 3
OS:Ubuntu 12.04 LTS
Openbabel 2.3

This is really more of an open babel problem but when trying to follow the tutorial instructions it fails to generate the pdb files from the sdf file. I have no problem converting individual files, but the batch script isn't working.

% foreach f ('cat /home/nick/Desktop/tutorial/VStutorial/VirtualScreening/etc/ligand.list')
? echo $f
? babel -isdf /home/nick/Desktop/tutorial/VStutorial/diversity.sdf -f "$f" -l "$f" -opdb \diversity"$f".pdb
? end
cat /home/nick/Desktop/tutorial/VStutorial/VirtualScreening/etc/ligand.list
==============================
*** Open Babel Error in FullConvert
Cannot write to diversitycat /home/nick/Desktop/tutorial/VStutorial/VirtualScreening/etc/ligand.list.pdb
0 molecules converted
1 errors

Thanks.
-Nick


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