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

["Lee, Jinhyuk" <>]

Dear All,

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?


Thanks alot





----Script

from modeller.automodel import *    # Load the automodel class                                                                      

log.verbose()
env = environ()
env.io.atom_files_directory = './'

templates=('3gb1')

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