As it turns out there were some problems with my .pdb file - missing chain label somehow. Once I fixed it everything works - sorry for the trouble.
Miles
Miles Pufall
Postdoctoral Scholar
Yamamoto Lab
UC San Francisco
Cellular and Molecular Pharmacology
Mail Stop 2280
600 16th Street, Genentech Hall S-574
San Francisco, California 94158-2517
(415)476-4480