I am trying to put secondary structure restraints (strand and sheet) to the MODELLER modeling. However, I found that most of the specified hydrogen-bonds between strands have not been satisfied in the final model. I understand that MODELLER tries to satisfy ALL the restraints and there may be some conflicts between my hydrogen-bond and other restraints.
My questions are: 1. do I have a way to make some restraints stronger than other restraints? 2. do I have a way to force some important restraints (like the beta-sheet) no matter whether they are conflicted with others?
Thank you very much!
The following is the python file I am using (please kindly point out any error in the file):
from modeller import * from modeller.automodel import * log.verbose() env =