Dear modeller...
..here is mine TOP file, I've tried to align it with both pdb from Brookheaven and genereted by Sybyl (free of hetero atoms and Ca) but it fails...
ERROR: dispers_247E> internal error : 1263 1267
recover____E> ERROR_STATUS >= STOP_ON_ERROR
INCLUDE
SET RR_FILE = '$(LIB)blosum62.sim.mat'
SET ATOM_FILES_DIRECTORY = './'
READ_MODEL FILE = '1I9B.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '1I9B', ATOM_FILES = '1I9B.pdb'
READ_ALIGNMENT FILE = 'xxxx.ali', ALIGN_CODES = ALIGN_CODES 'XXXX', ADD_SEQUENCE = ON
ALIGN2D
WRITE_ALIGNMENT FILE='xxxx_aln.ali', ALIGNMENT_FORMAT = 'PIR'
PDB file have 5 subunits and I try to align it...failed
Could I use another alignment programm? and hand-make my own alignment file? (I've tried one but it fails...)
Could you look at the alignment and top file???
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # comment to produce a large log file
SET ALNFILE = 'xxxx_ach.ali' # alignment filename
SET KNOWNS = '1I9B.pdb' # codes of the templates
SET SEQUENCE = 'XXXX' # code of the target
SET ATOM_FILES_DIRECTORY = './' # directories for input atom files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
CALL ROUTINE = 'model' # do homology modelling
STOP
>P;1I9B
structureX:1I9B: 1 :A: 1025:E:undefined:undefined:-1.00:-1.00
>P;XXXX
sequence:XXXX: : : : ::: 0.00: 0.00