Reply To: Docking a protein into a symmetrical complex

[Anonymous]

Btw, there are some caveats to using constraints with docking. First off, there are two types of constraints: site and distance. Right now, distance constraints are proper constraints objects, for which there is documentation here: http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/constraint_file.html. The only additional thing you should know for distance constraints is that for the “residue number” field, you can specify the pdb residue number and chain (e.g. 34A). We think this makes it more clear in the case of docking.

Site constraints are used to reward or penalize residues for being in the interface. Since this requires some additional information, these types of constraints are not proper constraints, that is, their parent is not a constraint. Because of this, site constraints currently have quite limited functionality, and I would recommend against using them until they have more functionality. If you want to try site constraints anyway, here are the details on the file format:
In a file with the extension .site:

ResNo Chain Penalty
ResNo Chain Penalty

ResNo is the pdb residue number, chain is the one letter pdb chain identifier and penalty is floating point number. A positive penalty is for residues that should not be in the interface, and a negative penalty is a reward for that residue being in the interface. Right now, this is applied as a step function (like I said, limited functionality), so please use with caution.