I have designed N-substituted peptides and want to use them as inpuct structures in ROSIE (NCBB Design). In order to prepare these inputs I tried to use relax application, however it doesn't work at all - output structure is not created and the only output I get is: core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom H12 in residue 17 B. Pass flag -ignore_zero_occupancy false to change this behavior, for every atom. I suppose it is due to the N-substitution. Is there any way to perform relaxation of such structures? I have tried using standard peptides as input structures for ROSIE, but the output structure from NCBB Design was not N-substituted.