- Suse linux 8.1
my files are:
me Top File
bioinf@bioinf4:/usr/local/bin/modeller6v2/work> more modelo.top 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 = '1f36A' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model (determines how many models tocalculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling
the files:
bioinf@bioinf4:/usr/local/bin/modeller6v2/work> ls -al total 188 drwxr-xr-x 2 bioinf users 216 2003-04-21 14:31 . drwxrwxrwx 5 wwwrun root 120 2003-04-21 14:28 .. -rw-r--r-- 1 bioinf users 281 2003-04-21 14:29 alignment.ali -rw-r--r-- 1 bioinf users 643 2003-04-21 14:31 modelo.top -rw-r--r-- 1 bioinf users 175446 2003-04-21 14:29 pdb1f36.ent
log file
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali All Rights Reserved
Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
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): 2003/04/21 14:31:58.119
TOP_________> 105 705 SET ALNFILE = 'alignment.ali'
TOP_________> 106 706 SET KNOWNS = '1f36A'
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 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/21 14:31:58.119 Closing time : 2003/04/21 14:32:01.072 Total CPU time [seconds] : 2.93
what is a problem?