Hi,

I need some help with optimization. I am confused what to do.

This is what i have done so far. 
On the first instance i used the scrip one to build the models. As i was not satisfied with the structural quality of the models, i used the second script below where i included a refinement command. Even then i couldn't get good models. So, i tried to a optimization script (third), to see if i can  build the models by iterative optimization. But that script just kept on failing. So, I am not sure what the problem is.. 

One: This one does not have the refine command

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

INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 2      # uncomment to produce a large log file
SET ALNFILE  = '2BCK.pir'      # alignment filename
SET KNOWNS   = '2BCK'               # codes of the templates
SET SEQUENCE = 'MesoA1'               # 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  = 3               # index of the last model
                                    # (determines how many models to calculate) 
SET HETATM_IO = on    
CALL ROUTINE = 'model'              # do homology modelling
STOP
--------------------------------------------------------------------------------------------------------------------------------------

Two: This has the refine command
INCLUDE                               # Include the predefined TOP routines

SET ALNFILE  = '2BCK.pir'      # alignment filename
SET KNOWNS   = '1BCK'            # codes of the templates
SET SEQUENCE = 'MesoA1'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../../atom_files' # dirs for input atom files
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
SET DEVIATION = 6.0
SET MD_LEVEL = 'refine_2'
#SET OUTPUT_CONTROL = 1 1 1 1 1
SET OUTPUT_CONTROL = 1 0 0 1 0

CALL ROUTINE = 'model'              # do homology modelling
---------------------------------------------------------------------------------------------------------------------------------------

Third:
INCLUDE
SET ALIGNMENT_FILE = '2BCK.pir', KNOWNS='2BCK', SEQUENCE='MesoA1'
# Very thorough VTFM optimization:
SET LIBRARY_SCHEDULE = 1, MAX_VAR_ITERATIONS = 300
# Very thorough MD optimization:
SET MD_LEVEL = 'refine1'
# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
SET REPEAT_OPTIMIZATION = 3, MAX_MOLPDF = 1E6
CALL ROUTINE = 'model'
---------------------------------------------------------------------------------------------------------------------------------------

I will appreciate if some one can help me. 

thanks in advance!! 

Harish