I am attempting to run some global docking simulations of two proteins. Not much is known about the interaction; however, I do know residues that are not involved in forming the protein-protein interface. Is there a way to put this information into a constraints file so that decoys that use these residues are not considered (or thrown out)?
I know that having the line:
SiteConstraint CA 16B A FLAT_HARMONIC 0 1 5
Is basically forcing the CA of residue 16 on chain B to be involved in the docking interaction with Chain A. Is there a way to make this command the inverse (say that resi 16 can't be involved in the interaction)?
On the rosetta dock tutorial on the Gray Lab webpage (http://graylab.jhu.edu/~mdaily/tutorial/constraints.html), they give an example of assigning penaltys to certain residues in a constraints file with the following format:
I understand that this will assigning a penalty of 20 to any decoy using resi 16, and filter any structures having a score greater than 10. I tried to implement this, but the following error was returned (I am assuming that the format for the Site Constraints listed on that webpage is not compatable with the current version of Rosetta):
ERROR: ConstraintFactory::newConstraint: 1 does not name a known ConstraintType --> check spelling or register new Constraint type in ConstraintFactory!
Thanks for your help!