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 ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
