I have the next problem, I execute "mod6v2 model-default.top" into directory "tutorial-model" and execute correctly
but the execute the next file obtain error
I have this alignment file:
******-----------------------**** my alignment file is:
>P1;1ety structureX:1ety:6:B:98:B:::: VNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVE QPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* >P1;sec1 sequence:sec1:1::93::::: VNSDVLTVSTVNSQAQVTQKPLRDSVKQALKNYFAQLNGQDVSDLYELVLAEVE QPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN*
*****------------------------------------------------------------------------**
and the log file is:
my log file is:
Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/16 11:55:50.106
TOP_________> 105 705 SET ALNFILE = 'alignment.ali'
TOP_________> 106 706 SET KNOWNS = '1ety'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1'
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 alignment.ali rdpir___270E> Error reading/processing file: alignment.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 : 2003/04/16 11:55:50.106 Closing time : 2003/04/16 11:55:53.073 Total CPU time [seconds] : 2.91
************----------------------------------------------****************************** My 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 = 'alignment.ali' # alignment filename SET KNOWNS = '1ety' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' # directories for input atom files 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
################################
what is a problem?, I have some problem in alignment file..?
Thaks...