“We ran full atom perturbation docking with an angle of 45 deg & a 10A distance. The results look as broadly distributed as the centroid blind docking, and none of the 10 structures with the most negative scores resemble the starting structure at all, or for that matter, each other. [And they all have scores with +/- 1 of each other – it’s as if these 2 proteins stick together pretty much at random]”
This means Rosetta thinks either A) they don’t stick, or 
it hasn’t had enough trajectories to find the right answer yet. 1000 seems like a small number of docking trajectories to me. I think 10,000 is still on the small side – remember that Rosetta is meant to be run on cluster supercomputers.
I’m not sure what you mean when you discriminate centroid from “full atom perturbation” docking. Generally, Rosetta wants to search different conformations with centroid mode, and then search within a conformational well with fullatom mode. The centroids are too coarse to get fine structure, and the fullatoms are too fine to allow efficient searching (almost all changes are rejected as clashing). I think doing the standard protocol (centroid then fullatom) is probably most appropriate (otherwise it wouldn’t be the standard)?
Writing constraints is fairly straightforward – had you seen this page? http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/constraint_file.html I don’t really know what you want by example. Here’s a vague one:
From experiment, you know that the backbone nitrogen on residue 34 is about 10-12 angstroms from the backbone hydrogen on residue 23. So, the first half of the constraint is an AtomPair constraint, which constraints interatomic distance:
AtomPair N 34 H 23
Next, you set up a function to score the distance defined by the AtomPair part. We’ll use a Bounded func, which defines a flat basin, with parabolic sides that become linear (you’ll have to plot the peicewise function to see what I mean)
BOUNDED 10 12 0.50 NOE ;dist 5.000 1.800
NOE and everything after is read as a comment.
So, the constraint line becomes:
AtomPair N 34 H 23 BOUNDED 10 12 0.50 NOE ;dist 5.000 1.800
Slap that in a file and pass it to docking and you’re good to go. (Don’t forget to also pass a constraint weight).