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It sounds as though the ligand structure contains atoms that are not recognised, for some reason. Are you able to inspect the structure file and figure out which atom(s) might cause a problem? It would help if you post a link to the ligand structure.
Yes, please upload the pdb then send us the link. You may want to use a file sharing site like: http://www.rapidshare.com/
Closing as "no longer relevant", since no new information provided.