What is a problem?? i need help...
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali All Rights Reserved
Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.4-4GB i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/10/17 15:00:00.125
TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali'
TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta'
TOP_________> 107 707 SET KNOWNS = '1f4hD'
TOP_________> 108 708 SET SEQUENCE = 'so34a0'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 399 CALL ROUTINE = 'getnames'
TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 117 513 SET ROOT_NAME = SEQUENCE
TOP_________> 118 514 RETURN
TOP_________> 119 400 CALL ROUTINE = 'homcsr'
TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1f4h-so34a0.ali openf5__224_> Open 13 OLD SEQUENTIAL /home/jpalacio/fasta/pdb1f4h.ent rdpir___270E> Error reading/processing file: 1f4h-so34a0.ali recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2205269 2153.583 2.103 Starting time : 2002/10/17 15:00:00.125 Closing time : 2002/10/17 15:00:03.672 Total CPU time [seconds] : 3.36
---------------------- teha align file is:
>P1;1f4hD structureX:1f4h: :D:: :::: ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* >P1;so34a0 sequence:so34a0: : : : ::: 0.00: 0.00 KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNEGPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN*
--------------------------
the top file:
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '1f4h-so34a0.ali' # alignment filename SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' SET KNOWNS = '1f4hD' # codes of the templates SET SEQUENCE = 'so34a0' # code of the target SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
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