Hi:
>From your output:
> rdpdb___303E> No atoms were read from the specified input PDB file:
> 1) Possibly because an incorrect/non-existent PDB file is specified.
> 2) Possibly because the segment is specified incorrectly in the
> alignment file or by the TOP variable MODEL_SEGMENT. That is,
> the beginning residue number and/or chain id in
> rdabrk__288W> Protein not accepted: 1
> rdabrk__290E> Number of residues in the alignment and pdb files are
> different: 166 0
> For alignment entry: 1
It seems like modeller is unable to read your pdb template file (it reads o
residues...), if you imported your file from MS-Dos/Win. that could be the
problem. (try opening the file in nedit and using the save as... option
looking that the MS-DOS format option is not selected in the "save as..."
menu).
I had the same problem, hope this helps.
Luis