Dear friends,

I got a initial model for my protein using modeller.Then i went for loop modelling for some of the regions that showed below the threshold value in verfiy3D program.

After the loop modelling i want to do energy minimization using optimize.top file.The following is the top file i used for energy minimization.

Example for: OPTIMIZE, SWITCH_TRACE # This will optimize stereochemistry of a given model, including # non-bonded contacts.

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE ='$(LIB)/par.lib' READ_MODEL FILE = 'topmodel6' SEQUENCE_TO_ALI ATOM_FILES= 'topmodel6', ALIGN_CODES = 'topmodel6' SEQUENCE_TO_ALI ADD_SEQUENCE =on, ATOM_FILES = ATOM_FILES 'topmodel6.ini', ; ALIGN_CODES = ALIGN_CODES 'topmodel6-ini' GENERATE_TOPOLOGY SEQUENCE = 'topmodel6-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'topmodel6.ini'

# Generate the restraints: MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'topmodel6.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'topmodel6.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 50 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 ENERGY

WRITE_MODEL FILE = 'topmodel6.B'

But it is not including heteroatoms in the energyminimized model.But the initial model has heteroatoms.

And also the module i am using is correct or i have to do any changes.Because more energy minimization also causes misthreading of the molecule.Kindly give me some suggestions.Expecting for your reply very eagerly.

Yours friendly, Senthil kumar.R