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...