I've been trying to assemble a poly-peptoid sequence using the make_pose_from_sequence function, however there seems to be an error in the way the polymer gets connected in the pose. For instance, the command:
make_pose_from_sequence(pose, "AAX[P02]AA", "fa_standard")
has no problem executing (P02.params works in other rosetta applications). However, when outputting the pose to PyMol it looks like the image attached. It would appear that there is an issue connecting the C-term of the last 2 alanines to the P02 N-term and subsequently overlaps them. Any ideas on how to fix this?