What does the `Alignment sequence not found in PDB file error mean?
When you give MODELLER an alignment, it also needs to read the structure of the known proteins (templates) from PDB files. In order to correctly match coordinates to the residues specified in the alignment, the sequences in the PDB file and the alignment file must be the same (although obviously you can add gap or chain break characters to your alignment). If they are not, you see this error.
