I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:
AtomPair CA 1 CA 41 HARMONIC 55.0 .1
My flags are:
During the run, I see the score output always says "atom_pair_constraint 10.000 0.000 0.000", and the final structures do not seem to be using the constraint I have given. However the final structure file does contain the energy breakdown table, and this table typically has an extremely high (>10,000) energy for the constraint. I do not understand how this constraint only seems to gain energy when the final structure is scored.
I know I am probably just missing some key parameter but I cannot figure out what. This is very confusing because I used Rosetta 2.5 and 2.4 about 2 years ago and as best I can remember, everything I am showing now would work with them. Does anyone have any advice on how I can fix this problem?
Thanks a lot,