Reply To: -score_app:linmin flag not working

[Anonymous]

To truly relax a protein into Rosetta’s scorefunction, use the relax application. Minimization cannot jump over energy barriers and does not perform any searching; relaxation actually searches through conformational space.

http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_relax_command.html

Minimization finds the closest energy well; relaxation searches for a closeby deep energy well.