On Mon, May 17, 2004 at 09:40:53AM +0200, Gianluca Croce wrote: > I'm a new user of modeller and I would like to know > which it is the measure unit used from mod6v2 for the > objective function? It is possible to have a correlation > between the unit of objective function and other units > (Kcal/mol, KJ/mol etc)?

The parameters and topologies used by Modeller for calculating the objective function are CHARMM files, so the energy is nominally in kcal/mol. However, the energy is strongly dependent on your choice of restraints, and should at best be considered a 'pseudo energy'; for example, it's probably unwise to directly compare the energies of two different proteins.

Ben Webb, Modeller Caretaker