On 3/13/15 9:06 PM, Arijit Ghosh wrote: > I made a good homology model with MODELLER, it's showing good > credibility in all the programs in SAVES server, but I want to do an > energy minimization before I go for docking some small ligands onto it. > > Please let me know if it is possible in MODELLER?

Modeller models are already minimized against its own scoring function. You could certainly try to do further minimization using a different scoring function, but it's debatable whether that would "improve" models.

Ben Webb, Modeller Caretaker