Hi Andrew,

The problem is that you don't have defined carboxyl O atoms in the last residue of your PDB, and since you didn't set:

READ_TOPOLOGY GENERATE_TOPOLOGY BUILD_MODEL

...which would read in missing atoms from the topology library, and rebuild the model, you got that warning message. It it not a big deal actually.

Best, Bozidar

> > > > Dear Bozidar > > Thanks for your assistance. Please find attached my I/O files. > > Andrew >> ----- Original Message ----- >> From: Bozidar Yerkovich mailto:bozidar@salilab.org >> To: Andrew Kiggundu mailto:andrew.kiggundu@fabi.up.ac.za >> Sent: Tuesday, January 21, 2003 4:46 PM >> Subject: Re: Problem with align2d >> >>> >>> Andrew, >>> >>> Can you please send me your I/O tar ball so that I can try to reproduce the >>> error here at mymachine. >>> >>> Thanks, >>> Bozidar >>> >>> >>> >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>