Trying something like the following in C++ Rosetta 3.3:
P = new core::pose::Pose();
Q = new core::pose::Pose();
for(size_t k=1; k<=P.n_residue(); k++)
I realize that I could be setting conformations, poses, etc, directly, but more generally I'm wondering what needs to be updated to get correct scoring in such cases?
use_nblist is false...
You should not need to update anything manually. Are the input poses identical in their residue sequence, bond lengths, and bond angles? What scorefunction terms are active?
That was it, bond angles/lengths were the problem. Thanks!