Regarding energy minimization using modeller
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
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
participants (2)
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Andras Fiser -
R Senthil Kumar