With regards to AtomPairConstraints and PDB numbering:
Almost nothing inside rosetta runs on PDB numbering. Nearly everything runs on 1-N numbering, where N is the total number of residues in the pose. This is because the Pose keeps said residues as a vector (indexed from 1). (You’ll notice vector1 everywhere instead of the C++ STL vector class – this is because the developers are mostly biological scientists, not computer scientists, and don’t like indexing from 0).
The only time you will EVER use PDB numbering in rosetta is if you see a function with pdb in the name. There is a class inside the pose which keeps track of pose versus PDB numbering and lets you convert between them. The resfile, for example, takes advantage of this.
The constraints framework does not use the PDB numbering options. The likely reason is that the developers who wrote the constraints use silent file input, not pdb input, and thus don’t think about PDB numbering at all. It would be possible to tweak the code to support this; it’s just as easy to renumber PDBs from 1. (There’s a script, chains.pl, that does this – I think it goes out with the releases).
With regards to dock_pert – I’m reasonably certain that the values you give here are maxima, not settings. In other words a value of 8 will allow 7, 6, 5, etc… So you may not need to try lots of different perturbations – just leave it at your maximum and run more. I’m not sure I understand your question so I may not be addressing it well.