I am trying to use Rosetta 3.3's Ab-initio relax program to fold a protein with cross-linked lysines. I am trying to use distance constraints to represent the cross links, but every time I try to run Ab-initio on the following constraint file, I get the error "Exception : Atom NZ 26 not found". Does anyone know why this might be happening?
AtomPair NZ 26 NZ 27 BOUNDED 5.26 8.17 0.50 NOE
AtomPair CA 86 CA 87 BOUNDED 4.72 10.52 0.50 NOE
AtomPair CA 99 CA 100 BOUNDED 7.74 13.56 0.50 NOE
AtomPair CA 39 CA 53 BOUNDED 15.62 16.40 0.50 NOE
Chances are 97% that it's because abinitio has a centroid phase; during the centroid phase the reduced sidechain representation only has CB and a CEN atom; NZ isn't present (thus the error). Try constraining on CB or passing two separate constraint files for fullatom and centroid mode. (The flags would be something like fa_cst_file, fa_cst_weight, cen_cst_file, cen_cst_weight; I forget exactly what they are and I'm not sure if they'll work separately for abinitio anyway.)