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, openbabel-discuss-requ...@lists.sourceforge.net wrote:
> Message: 5
> Date: Wed, 16 Feb 2011 11:33:19 -0800
> From: Felix Grun <fg...@uci.edu>
> Subject: [Open Babel] Use of wild card characters in iBabel GUI ?
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <ade9d7cc-d681-4145-b900-ff2ceeaf4...@uci.edu>
> 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
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