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