Hi Senthil,
try to switch on the necessary input output command
SET HETATM_IO=on
FAQ 15 page 110 in the manual
With respect to your second question: I do not believe that reoptimizing the model is going to improve the equality of it. Probably just on the contrary.
Best wishes, Andras
R Senthil Kumar wrote: > > 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