Dear Bozidar,
I had problem when trying to get some a protein model.
What do I have to do? I used the PIR alignment format
also.
My Top file is:
INCLUDE # Include the
predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to
produce a large log file
SET ALNFILE = 'alignment.seg.pap' # alignment
filename
SET KNOWNS = '1h9p' # codes of the
templates
SET SEQUENCE = '1drg' # code of the
target
SET ATOM_FILES_DIRECTORY = './:../atom_files' #
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
The alignment file seems to be ok:
Kind, OS, HostName, Kernel, Processor: 4, Linux
localhost.localdomain 2.4.18-6mdkenterprise i686
Date and time of compilation : 07/05/2002
17:30:36
Job starting time (YY/MM/DD HH:MM:SS): 2002/07/18
13:08:16.425
TOP_________> 105 705 SET ALNFILE =
'alignment.seg.pap'
TOP_________> 106 706 SET KNOWNS = '1h9p'
TOP_________> 107 707 SET SEQUENCE = '1drg'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY =
'./:../atom_files'
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.seg.pap
Dynamically allocated memory at amaxbnd
[B,kB,MB]: 2560929 2500.907 2.442
openf5__224_> Open 11 OLD SEQUENTIAL
alignment.seg.pap
Read the alignment from file : alignment.seg.pap
Total number of alignment positions: 0
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1h9p 0 1
2 1drg 0 1
TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
check_a_337E> Structure not read in: 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1
1
Dynamically allocated memory at finish
[B,kB,MB]: 2560929 2500.907 2.442
Starting time
: 2002/07/18 13:08:16.425
Closing time
: 2002/07/18 13:08:17.598
Frederico Moreno
_______________________________________________________________________
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