(note: I have installed modeller6v2 in Linux Suse 8.1.    When execute modeller with the examples , modeller execute correctly .   If the files "model-default.top" and "alignment.ali" in the directory "tutorial-model" are copy in other directory and execute the process (mod6v2 model-default.top) run correctly obtain the new model for target sequence )


hi

I have a problem to run modeller

I create  my alignment file (alignment.ali) and top file (model-default.top) ,but  to run "mod6v2 model-default.top" the log file to show the not execute the process.  and the log file no show errors. 

which can  be the problem?

the files are:

alignment.ali

C; A sample alignment in the PIR format; used in tutorial
>P1;1f36A
structureX:1f36:10    :A :98  :A : : : :
VLTVSTVNSQDQVTQKPLRDSVKQALENYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN*
>P1;sec1
sequence:sec1:1    :A :89   :A : : : :
VLTVSTVNSQAQVTQKPLRDSVKQALKNYFAQLNGQDVSDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN*

model-default.top

# Homology modelling by the MODELLER TOP routine 'model'.
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' # 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


model-default.log

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): 2003/04/17  14:05:48.759
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
 
Dynamically allocated memory at          finish [B,kB,MB]:      2200483    2148.909     2.099
Starting time                                            : 2003/04/17  14:05:48.759
Closing time                                             : 2003/04/17  14:05:51.710
Total CPU time [seconds]                                 :       2.87

the log file no show errors and show that the process is not execute.

which can  be the problem?  I need Help

The modeller have other file where save logs?

thanks...