Hi Pasquale,

If your structure all got put into a single residue named UNK, that typically means that your file was missing the @SUBSTRUCTURE section (http://www.tripos.com/mol2/mol2_format33.html#1370).  There is an entry in our bug database (#3518) for better handling of files with missing @SUBSTRUCTURE sections.  I will add your name to that report so you'll know when it gets fixed.  For now, you will have to edit your file and add an @SUBSTRUCTURE section "by hand".

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu