Dear Modeller users,
I am using Modeller6.2. To test the quality of the model, I tried to build
a model for a protein (300 aa)using its crystal structure as the template.
With MD_level = refine_1 or 3, the backone RMSD is 0.25-0.3, which is
great. However, in both refinement conditions, the RMSD of the heavy
atoms of the backbone plus chainchains is close to 3.0 angstroms. By
visual inspection of the superimposed structures, the sidechains of the
model indeed do not overlap with its crystal structure so well.
My questions: Did you observe similar result? How do you refine the
sidechains? MD simulation of the sidechains with backbone
restrained (in explicit water solution) is in my mind. I would
appreciate your suggestion and experience.
Regards,
Jain Hui Wu
Lady Davis Institute
McGill Universty