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
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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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I will appreciate if some one can help me.
thanks in advance!!
Harish