I'm trying to perform ALIGN2D of a target sequence with the sequence of a protein with with X-ray structure, but I keep on getting errors. The protein has several subunits, and I want to align with subunit A only.

The top file is:
READ_MODEL FILE = '1HZX.pdb', MODEL_SEGMENT '@:A' 'X:A', OUTPUT_CONTROL = 1 1 1 1
SEQUENCE_TO_ALI ALIGN_CODES = '1HZX'
READ_ALIGNMENT FILE = 'hp2y1.seq', ALIGN_CODES = ALIGN_CODES 'hp2y1', ;
ADD_SEQUENCE = on
READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/modlib/top_heav.lib'
ALIGN2D
WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.pap', ALIGNMENT_FORMAT = 'PAP', ;
ALIGNMENT_FEATURES = 'indices helix beta'

The error reported is:
...
# Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
1       1HZX     641      3        1HZX undefined
2      hp2y1     373      1       hp2y1
TOP_________>     4    4 READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/mo;
                      dlib/top_heav.lib'

openf5__224_> Open       11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//as1.sim.mat
rdrrwgh_268_> Number of residue types:       20
dispers_247E> Internal error:      640      641
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     23066567   22525.945    21.998
Starting time                                            : 2001/11/12 13:53:59.313
Closing time                                             : 2001/11/12 14:41:13.406
Total CPU time [seconds]                                 :       0.00

Thanks, Dan

-- 
Dan Thomas Major (at Dr. B. Fischer's lab)
Bar-Ilan University 
Ramat-Gan, Israel