it's hard to say what goes wrong as your email does not contain the error message or your input files, but I would guess the line
X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: :
causes the problem, it should read like this:
structureX:1L9H:37 : :307 : :rhodopsin:Bos Taurus: :
You should consult the modeller manual about the correct input file formats, to make sure there is not anything else wrong with your alignment:
I hope that helps.
Best wishes, Thorsten Schweikardt Molekulare Biophysik Universität Mainz