Dear sir i have just started using modeller7v7 but have landed in to some problems.i have a few doubts 1. which directory should i place the top files, ali files and the pdb files. i placed top files in the bin, pdb files in atom-files directory. and tried to run the command, but it shows this error
MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2004 Andrej Sali All Rights Reserved
Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, Win2000 build 2195 Service Pack 4, PROJECTBT, uni, x86 Family 15 Model 2 Stepping 9 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/12/27 13:26:51.093 TOP_________> 109 749 SET ALNFILE = 'seqalin.ali'
TOP_________> 110 750 SET KNOWNS = '1ocs'
TOP_________> 111 751 SET SEQUENCE = 'yhr'
TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 113 753 SET STARTING_MODEL = 1
TOP_________> 114 754 SET ENDING_MODEL = 1
TOP_________> 115 755 CALL ROUTINE = 'model'
TOP_________> 116 419 CALL ROUTINE = 'getnames'
TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 121 538 SET ROOT_NAME = SEQUENCE
TOP_________> 122 539 RETURN
TOP_________> 123 420 CALL ROUTINE = 'homcsr'
TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 fullfn__230E> File not found: seqalin.ali Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2004/12/27 13:26:51.093 Closing time : 2004/12/27 13:26:52.078 Total CPU time [seconds] : 0.97
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