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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