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' ------------------------------------------------------------------------------------------------