SDF to mol2
This can be done using MOE either in batch mode or using the GUI. Open the sdf file in the MOE database viewer and use the command DBV | Compute | Energy Minimize.
In command line or batch mode 'db_Minimize' command can be used. See the moe tutorial at file:///c:/moe/html/mdb/db3d.htm
You can add hydrogens, assign partial charges as well as convert the 2D molecule to 3D conformation using this. A force field has to be chosen first using the Potential command.