script file to obtain improved protein model?

[Antonello Romani <>]

Dear users,

I have set my input files to obtain an improved model of my protein. I wolud like to know if
these files are right or wrong and if there are other stuff that I have to do to improve
quality of my protein (I test it with Procheck or What_Check)

----------------------------------Build model---------------------------------------------------
# 

INCLUDE                             # Include the predefined TOP routines
SET ALNFILE  = 'xxxx.ali'      # alignment filename
SET SEQUENCE    = 'myprot' 
SET LIBRARY_SCHEDULE = 1
SET MD_LEVEL = 'refine3'
SET FINAL_MALIGN3D = 1
SET REPEAT_OPTIMIZATION = 15
SET RSTRS_REFINED = 2
SET MD_RETURN = 'MINIMAL'
SET KNOWNS   = 'template' # codes of the templates
SET ATOM_FILES_DIRECTORY = 'xxxxxxxxxx' # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model 
SET ENDING_MODEL  = 15
# Do a mixed minimization

# Do homology modeling
CALL ROUTINE = 'model'              
------------------------------------------------------------------------------------------------



----------------------------------Optimize stereochemistry--------------------------------------
# 

INCLUDE                             # Include the predefined TOP routines
READ_TOPOLOGY FILE ='$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = 'myprot.pdb'
SEQUENCE_TO_ALI ATOM_FILES = 'myprot.pdb', ALIGN_CODES= 'myprot'
SEQUENCE_TO_ALI ADD_SEQUENCE = on,ATOM_FILES = ATOM_FILES 'myprot',ALIGN_CODES= ALIGN_CODES 'myprot'
GENERATE_TOPOLOGY SEQUENCE = 'myprot'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
WRITE_MODEL FILE = 'myprot.ini'
 
# GENERATE THE RESTRAINTS 

       MAKE_RESTRAINTS  RESTRAINT_TYPE  =  'stereo'
       WRITE_RESTRAINTS  FILE  =  'myprot.rsr'
       ENERGY  DYNAMIC_SPHERE  =  on
       SWITCH_TRACE  TRACE_OUTPUT  =  1,  FILE  =  'myprot.trc'
       ENERGY DYNAMIC_SPHERE = on
       OPTIMIZE DYNAMIC_LENNARD =on
       OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000
       OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 10000,MD_RETURN = 'MINIMAL',EQUILIBRATE =20,;
       		MD_TIME_STEP =2.0, CAP_ATOM_SHIFT = 0.1, RAND_SEED = -3065
       OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000
       ENERGY
       
       WRITE_MODEL FILE= 'myprot_optimize.pdb'
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