Hi, I've been using Rosetta to generate models of antibody-antigen interactions. I'm using the 2014wk05 release to do the following: I use an antibody downloaded form pdb (4KVN) remove the chain A, hetatm and waters in pymol then load in the new antigen (generated using I-Tasser and free of heteroatoms etc.), this joined file is then saved and fed in to rosetta scripts with the following flags:
This is the Docking.xml I'm using:-docking -dock_pert 8 5 -spin 1 -randomize1 -docking_centroid_outer_cycles 10 -docking_centroid_inner_cycles 50 -docking:dock_mcm_trans_magnitude .1 -docking:dock_mcm_rot_magnitude 1 -nstruct 100 -database /path/to/rosetta_2014wk05_bundle/main/database -linmem_ig 10 -ex1 -ex2 -ex1aro -overwrite -parser:protocol '/path/to/parameters_rosetta/docking.xml' -packing:repack_only -restore_pre_talaris_2013_behavior -out:pdb -partners HL_A -use_input_sc
This had been working pretty well up until my last few models where I am now getting the following error:MOVERS >
ERROR: Unable to set up interface foldtree because there are no movable jumps ERROR:: Exit from: src/protocols/docking/util.cc line: 289I've tried a number of different flags, I tried adding a -native flag but nothing seems to help. The only other thing different about these files is that they contained a hydoxylated PRO resn so I had to modify the patches.txt to add a patches/pro_hydroxylated_case1.txt line to correct the initially error I was getting. So my guess is that it has something to do with that but after a few days of searching and attempting solutions on my own I've come up empty. Any guidance is appreciated and I'm happy to share the pdb file I'm using if that helps. On a more general note I'm still sorting things out with flags and options so if there are any optimized options anyone has come across from generating antibody-antigen models like this please feel free to give your feedback, any help is appreciated.