I would like to design a protein sequence using a mixed fixbb-relax protocol.
Basically, I want to do something like in this publication: http://www.sciencedirect.com/science/article/pii/S0969212612001517
(The idea is to iterate between fixbb and relax protocols as long as the Rosetta energy difference between models is bigger than 1.0 REU)
Does anybody have an idea how to use RosettaScripts to implement this?
I understand that my script(below) runs fixbb, takes the best trajectory and inputs it into relax and I get output model that has gone through fixbb and relax only once. But I would like more cycles to occur and each time energy difference between cycle i and i-1 should be calculated to determine if next cycle should be made.
I attach what I have done so far, XML file (as txt attachment, no other way), command and flags:
default.linuxgccrelease @flags_designrelax -out:file:silent results.out -parser:protocol design_relax.xml