The PPM server calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input. It can be applied to newly determined experimental protein structures or theoretical models. Many membrane-associated proteins from the PDB have already been pre-calculated and can be found in the OPM database.
Find Orientation of Protein in Membrane
  (topology should be indicated for N-terminus of the first subunit in PDB file)
Include heteroatoms, excluding water and detergents, for positioning in membrane:
  (please include heteroatoms for peptides with non-standard amino acid residues)

Please see  instructions

Lomize M.A., Pogozheva I,D, Joo H., Mosberg H.I., Lomize A.L. OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res., 2012, 40(Database issue):D370-6