Regarding energy minimization using modeller

[R Senthil Kumar <>]

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(is this top file can be used for energy minimization). 
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.How to include heteroatoms in the file. 

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