If you are using YASARA-Structure, you will have access to a spectrum of force fields and built-in macros for doing energy minimizations. For small molecules, energy minimizations are usually carried out in a vacuum using the NOVA force field. For proteins, energy minimizations are usually carried out with one of the AMBER-derived force fields in aqueous solution -- the built-in macros will take care of filling the cell with water and ions appropriate for the selected pH and ionic strength.