Frederico,

Please check if your ali file is in the right directory? You are simply not reading the file in....

Best, Bozidar

On Thu, 18 Jul 2002, Frederico Moreno wrote:

> 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 > > > _______________________________________________________________________ > Yahoo! Encontros > O lugar certo para encontrar a sua alma gêmea. > http://br.encontros.yahoo.com/ >