My pose has DNA strands and I am trying to constrain the blunt ends.
Each DNA chain is numbered starting from 1. Why can't Rosetta find the atoms?
Here is my constraint:
AtomPair C1* 1C C1* 35D HARMONIC 12.028 1.00
And here is the error:
[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom 'C1* 1359' not found
Try C1' instead of C1* and see what happens. That's what Rosetta expects the atoms to be named (you can look at Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/nucleic/dna/*params to see what atom names Rosetta expects). It's likely the PDB reader has an override to accept * for ' for nucleic acids, but that logic doesn't inform the constraints file reader.
If changing ' -> * in the constraints file doesn't work, try doing it in the PDB, too.
Using C1' rather than C1* worked.