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

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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

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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'

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