> modified?after doing this the energy is far different from VASP result,why
I’m not sure why you’d be concerned that UFF (a classical method) has a different energy than VASP (a quantum method). Moreover, the current force field implementation in Open Babel does not use periodic boundary conditions, and your VASP input clearly has a unit cell. > p=ff.GetCoordinates(mol) At the moment, I can’t comment on your case, but if you don’t want to optimize the geometry, don’t get updated coordinates from the force field. If you just want the energy, you don’t need this call. > CORRECTED COORDINATION FOR ANGLE 3-1-5 (IDX)... WAS 6 NOW 5 This isn’t changing the geometry. It’s a warning that while the UFF parameters are designed for 6-coordinate metals, in your fragment, you have some which are detected to be 5-coordinate. So Open Babel is substituting octahedral bending parameters for trigonal-bipyramidal parameters. That may or may not be what you want (e.g., maybe the bonding is incorrect). Hope that helps, -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
