Hi Everybody here,
 
I am new to the modelling world and have successfully installed Modeller v6.2 onto windows2000 PC. Got the tutorial to run fine. started modelling my protein. A series of errors I managed to sort out, using the manual, practical article, the FAQ and this list's archive. However, I have had to send in this somewhat simple problem that may have been addressed several times on the list but I have failed to figure out how to get out of it.
 
I am trying first to align two sequences using align2d like so:

READ_MODEL FILE = '1eqk.pdb'                                                                                SEQUENCE_TO_ALI ALIGN_CODES = '1eqkA'                                                                         READ_ALIGNMENT FILE = 'PapCys.ali', ALIGN_CODES = 'PapCys', ADD_SEQUENCE = ON                                         ALIGN2D                                                                                                      WRITE_ALIGNMENT FILE='PapCys-1eqk.ali', ALIGNMENT_FORMAT = 'PIR'                                                    WRITE_ALIGNMENT FILE='PapCys-1eqk.pap', ALIGNMENT_FORMAT = 'PAP'

Then I get the following error message:

iatmcls_286W MODEL atom not classified: ALA:OT1 ALA                                                            iatmcls_286W MODEL atom not classified: ALA:OT2 ALA

I have checked all lib files and ALA seems well defined, However, I belive there may be a problem in the ieqk.pdb file which have not touched sine downloading from the PDB database.

Can anybody help

Andrew