The following one after the main text is my script to get energies.
I put my restraint file (L001.rsr) and my initial structure (init.pdb).
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.
However, Modeller complained like that.
> Summary of failed models: T0388.B99990001.pdb ddihedr_262E> Central bond too short: 0.0000
Is there any other scripts to do the same job?
from modeller.automodel import * # Load the automodel class
log.verbose() env = environ() env.io.atom_files_directory = './'
a = automodel(env,alnfile = 'L001.ali',knowns= templates,sequence='L001',inifile='init.pdb',csrfile = 'L001.rsr')
a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.max_molpdf=10000000000000.0 a.max_var_iterations=0 a.make() # do homology modelling
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