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:>
>> To: Andrew Kiggundu <">mailto:>
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
--
Bozidar Yerkovich, PhD
Rockefeller University
New York, NY, 10021, USA
212-327-7206
http://salilab.org/modeller