Re: [modeller_usage] How can I get restraint energies of initial structure without building a model.

[Modeller Caretaker <>]

On 1/26/10 5:21 PM, Lee, Jinhyuk wrote:
> I want to see the energies on initial structure without building
> (energy minimization) a model so that I include
> "max_var_iterations=0" in the script.

That won't disable energy minimization, since you'll still be doing
MD/SA model refinement. It will only disable the initial CG local
optimization. Running MD on a non-relaxed structure could well result in
the sorts of optimizer failures you're seeing.

Note also that the initial model is randomized (so that you get
different results from building multiple models). So the energy wouldn't
be of your initial structure anyway.

You can get the energy of your initial structure using a script like:

a = automodel(env, ...)
a.make(exit_stage=1)
a.rd_restraints()        # Make sure restraints are read in
atoms = a.select_atoms() # Get all atoms marked for optimization
atoms.energy()           # Get the energy of initial structure

	Ben Webb, Modeller Caretaker
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