Here is the seq_search.top file:
SET SEARCH_RANDOMIZATIONS = 100
SET FILE = 'TvLDH.ali'
READ_SEQUENCE_DB
SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON
If you want to use that TOP file, you should change it to:
SET SEARCH_RANDOMIZATIONS = 100
SET FILE = 'TvLDH.ali'
READ_SEQUENCE_DB
READ_ALIGNMENT ALIGN_CODES = 'TvLDH'
SEQUENCE_SEARCH DATA_FILE = ON
SEQUENCE_SEARCH was changed in Modeller 8v0 to take a previously-read
alignment file (READ_ALIGNMENT) as input, rather than reading the
sequence itself. See the last entry in the 8v0 changelog at
http://salilab.org/modeller/manual/node20.html