Re: Regarding energy minimization using modeller

[Andras Fiser <>]

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

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras