Hi, On Thu, Mar 8, 2012 at 9:30 PM, Fouad Ballout <fouad.ball...@rub.de> wrote: > Hi there, > > I have problems with generating conformers for a particular molecule using > openbabel. Following the openbabel documentation I've used the following > command line > > obabel input.xyz -O output.xyz --conformer --systematic --ff GAFF
The systematic conformer search only writes out the lowest energy conformer. > in order to find all local stable conformers using GAFF but without success. > The output just contains one structure. The same happens if I use a command > line similar to that appearing in the documentation: > > obabel input.xyz -O output.xyz --conformer --nconf 50 --score energy Using the genetic algorithm, it's possible to write out all 50 conformers if you add the --write-conformers parameter IIRC. Check the babel -H help information to ensure it's the right parameter. > What is wrong with these commands? By the way how does openbabel perform > this systematic conformational search? The systematic search is done by rotating all bonds and selecting the lowest energy conformer. > I would really appreciate it if > someone could help me out with this. Tim > Best regards > Fouad Ballout > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
