align2d warnings

[Alex Brown <abrown@nimr.mrc.ac.uk>]

Hi.

A small problem with the align2d script from the TvLDH tutorial 
examples. The align2d.top script is as follows:
READ_MODEL FILE = '4mdh.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '4mdhA'
READ_ALIGNMENT FILE = 'TvLDH.ali', ALIGN_CODES = ALIGN_CODES 'TvLDH', 
ADD_SEQUENCE = on
ALIGN2D
WRITE_ALIGNMENT FILE='TvLDH-4mdhA.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='TvLDH-4mdhA.pap', ALIGNMENT_FORMAT = 'PAP'

Running this produced the following warnings in the align2d.log file :

iatmcls_286W> MODEL atom not classified:  ALA:OT1  ALA
iatmcls_286W> MODEL atom not classified:  ALA:OT2  ALA
pdbnam__217W> Filename for PDB code not found:  4mdhA
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        1
mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read 
one.
This seems to indicate that the template file or template sequence 
cannot be found. However, the alignment goes ahead and is fine (ie. both 
target and template sequences were present). Could someone please 
explain.
As usual, I'm running MODELLER 6v2 on Mac OS/X Darwin.

Cheers,

Alex.