Molecular systems in Sire can be loaded from AMBER-style input files. The molecule is described primarily with two files: the prmtop (or prm7) file that holds all the parameters and the inpcrd (or rst7) that contains the coordinates of the atoms. Functionality in Sire has been extended to include new features that support parsing of the QUBE pdb and xml input files and that support the OPLS-type potential energy functional form (Figure ).