As far as I have understood, you are going to calculate LaTiO3 doped with Y atoms. LaTiO3 perovskite is rather well investigated compound, so you can find a lot of information about its atomic positions and even plotted band structures. For example, in the paper http://arxiv.org/pdf/cond-mat/0412063.pdf, both LaTiO3 and YTiO3 are considered including references to structural data. Then you have to build a supercell in which replace some La atoms by Y according to the concentration you are going to reach.

ADF, GAUSSIAN, OPenmx etc.