Dear Friends, I got my initial model for my protein using MODELLER 9v1 which was further assessed by DOPE potential in MODELLER to evaluate model fold and with the program PROCHECK and VERIFY3D. In Ramachandran plot my model showed 93.9% core 5.8% allow .0% gener .3% disall region and 3 bad contacts. Verify 3d data showed above 90% of the residues had an averaged 3D-1D score > 0.2. Please suggest whether I shall have to do energy minimization and if energy minimization is necessay also suggest how it is possible and which parameter I shall have to use for energy minimization.

Best regards.