Dear Rosetta Community,
I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.
However I am facing the following error:
ERROR: Unable to auto-assign a lower anchor for the loop to be closed. Check that the first residue is connected to something that isn't in the loop to be closed and isn't a tail residue. ERROR:: Exit from: src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc line: 1323 protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol: File: src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc:1323
I am running my XML script on version Rosetta2020.03 using the following command:
module load apps/Rosetta/2020.03/intel2019 mpirun -np 1 $ROSETTA_BIN/rosetta_scripts.mpi.linuxiccrelease -parser:protocol nothing.xml -s 2LUR0.pdb -nstruct 1 -overwrite
I am attaching the XML script ("nothing.txt") for reference. I've tried to verify my script from the available Rosetta GeneralizedKIC documentation, and referred to papers from Bhardwaj, G., et al. (2016); Mulligan, V. K., et al. (2021) and a few others but I am unable to rectify. Any help will be appreciated.
A snippet from the code:
<AddResidue res_index="1" /> . . . <AddResidue res_index="29" /> <SetPivots res1="1" res2="16" res3="29" atom1="CA" atom2="CA" atom3="CA" />