For RosettaLigand with some backbone flexibility, I have experimented with adjusting the harmonic_Calphas value from 0.3 to 0.5, 1, and 2.5. I have noticed that there is more backbone motion when I do this. However, is this advisible to adjust? I understand that this value imposes harmonic restraints on the backbone during the minimization step. Why impose these restraints at all? I know the default is 0.3, but how much can this value be safely changed?
I am also curious how many residues around the ligand are allowed to relax in this manner. The paper (2008) says that only a few residues move - but how exactly is this value determined? I am curious because I am running a series of RosettaLigand docking runs on different conformations of a protein (generated by homology modeling from multiple templates) and I would like to know what value to set the harmonic_Calphas value in the flags file to in order that the protein explore most of the conformations existing between the different conformations I've generated.
Eric Barker's laboratory