problem with check_alignment

[JP <>]

-  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?