Upcomming OpenBabel 2.2 release

OpenBabel 2.2 will be released soon. In the past 9 months since the 2.1.1 release, the force field code has really improved.

Two new force fields are available in 2.2. The first is MMFF94, a force field that can be used for drug like molecules and ligand-protein interactions. Although this force field could be used for proteins themselves, protein specific ones like AMBER would be more suited, especially for performance reasons. The implementation is validated using the MMFF94 validation suite and the results are available here. Some special cases remain problematic such as bridged rings and emperical rules when parameters are missing. However, the errors are so small and rare that it is suited for most applications.

The second new force field, implemented by Geoff, is UFF. This force field has parameters for the entire periodic system and is therefore a valuable addition to the list. Bob Hanson has also ported UFF from openbabel to JMol. Towards OB 3.0 a biomolecule force field like AMBER will probably be added.

Another great improvement is the performance. The numbers on the updated wiki page speak for themselves. Minimizations run about 100 times faster!

This will be the first release with the OBBuilder class. This allows openbabel to generate 3D coordinates with a fragment based approach. The database with fragments was derived from Zinc database by Geoff. Stereochemistry will not be taken into account for now, but it's a great start.