>> babel -isdf 1.sdf -o mol2 2.mol2 --writeconformers --gen3D --nconf 4 >> --weighted > > The result, however, is a file name '4' instead of 2.mol2. If I remove the > --nconf, i do get 2.mol2 (one conformation). Is that a bug or am I using the > command incorrectly?
We highly recommend using the newer “obabel” program since the command-line is easier. obabel 1.sdf -O 2.mol2 --gen3d --conformer --weighted --nconf 4 But this might not do what you want. This will sample 4 conformers and write out the lowest in energy. Do you want 4 low-energy conformers output to the mol2 file? BTW, for input and output formats, obabel can guess the file type from the extension, so ‘-isdf’ and ‘-omol2’ are optional. Hope that helps, -Geoff ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
