-  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?