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
Extensions : :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted: 1
mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read
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
As usual, I'm running MODELLER 6v2 on Mac OS/X Darwin.