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From: <chr...@bt...> - 2011-02-18 15:46:45
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I notice from the command line you use m -gen3D but iBabel outputs m --gen3D And according to the babel help it should be m --gen3D Also try clicking the "Use Terminal" checkbox on the bottom left of the GUI and see what happens. I'll also investigate further Chris On 18 Feb 2011, at 15:14, ope...@li... wrote: > Message: 5 > Date: Wed, 16 Feb 2011 11:33:19 -0800 > From: Felix Grun <fg...@uc...> > Subject: [Open Babel] Use of wild card characters in iBabel GUI ? > To: ope...@li... > Message-ID: <ADE...@uc...> > Content-Type: text/plain; charset=us-ascii > > Hi, > > I'd like to use iBabel 3.0beta and Open Babel 2.3.0 running on my iMac OSXv10.6 to batch convert .mol files to .pdbqt files for virtual docking. > > If I change directory to a desktop folder containing my structures, I can successfully use "babel" from the terminal to batch convert using the wild card character * for the input file. > > biologix:~ farpelix$ cd /Users/farpelix/Desktop/Docking/Ligands/Mol_Files/ > biologix:~ farpelix$ babel -imol *.mol -opdbqt -m -gen3D > > However when I use the GUI in iBabel, I cannot use wild card characters in the File Input field. Instead I get an "OpenAndSetFormat" error message in the terminal as follows: > > /usr/local/bin/babel -imol '/Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol' -opdbqt '/Users/farpelix/Desktop/Docking/Ligands/PDBQT/ligand.pdbqt' -m --gen3D > > -bash: ?: command not found > biologix:~ farpelix$ /usr/local/bin/babel -imol '/Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol' -opdbqt '/Users/farpelix/Desktop/Docking/Ligands/PDBQT/ligand.pdbqt' -m --gen3D > ============================== > *** Open Babel Error in OpenAndSetFormat > Cannot open /Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol > 0 molecules converted > 1 errors > > What is the correct syntax for using wild card characters in iBabel, or do I need to change any settings for babel ? > > Any help would be appreciated. Thanks. > > Felix Grun |