I think I have found the problem but I don´t know how to solve it.
The residue in question is an HETATM; I mean that where the sequence
indicates a SER the pdb file has an HETATM (CSO). How can I solve it?
Simply, it means that your alignment does not match your PDB. Obviously
they have to match exactly, otherwise Modeller will not know how to
generate its restraints. If you can't figure it out, you should post the
PDB code and your alignment, as it's hard to say anything more without
seeing these.
Ben Webb, Modeller Caretaker
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