This is a continuation of an earlier thread, but I am still having trouble getting the surface_docking application to accept my inputs of a protein and ice surface. After correcting issues with hydrogen naming and now using the -ignore_waters false flag so that rosetta does not delete the ice surface, I am still getting the following error (this was all the error output):
surface_docking.linuxgccdebug: src/protocols/surface_docking/SurfaceDockingProtocol.cc:358: void protocols::surface_docking::SurfaceDockingProtocol::split_protein_surface_poses(const core::pose::Pose&, core::pose::Pose&, core::pose::Pose&): Assertion `valid_surface_pose( pose )' failed.
Got some signal... It is:6
Process was aborted!
I assume this means it does not like the surface geometry or the surface vector. Anyone have any troubleshooting suggestions?
That error would occur when there are more than two "chains" in the input pose. For surface docking to work all of the surface atoms need to be considered a single "chain".
What does your input structure look like? Are all the ice atoms getting the same chain letter designation? Do you have any TER records within the ice atoms?