Hi All,
 
After sending e-mail yesterday, I received several e-mails and all told me I should see the .log file in the same directory. But I am sure there is no .log file in the directory. I am using MODELLER 6v2 for Windows and my operation system is Window 2000. I run "mod model-default" in windows command prompt "C:\mod6v2\examples\tutorial-model>". Following is the model-default.top file:
 
# 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   = '5fd1'                               # codes of the templates
SET SEQUENCE = '1fdx'                               # 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
 
After running "mod model-default", I only got six files: "1fdx.V99990001, 1fdx.D00000001, 1fdx.B99990001, 1fdx.sch, 1fdx.rsr and 1fdx.ini. I can open the 1fdx.B99990001 by a viewer.
 
Thanks for all your help,
 
Dong