IndexError in dl_interface_design.py

[hklz]

Hello, I'm encountering an issue/need assistance and I'm hoping to get your guidance.

I have activated the dl_binder_design environment and run command like: ~/autodl-tmp/dl_binder_design/mpnn_fr/dl_interface_design.py -silent lhyal_binder.silent -output_intermediates -checkpoint_path ~/autodl-tmp/dl_binder_design/mpnn_fr/ProteinMPNN/vanilla_model_weights/v_48_020.pt the .silent file is the .pdb file in the output of the RFdiffision.

But I get the following error report as follows.

core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 31640 bytes
protocols.relax.FastRelax: CMD: accept_to_best  726.868  22.7618  0.596962  0.55
core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph
core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 266 edges requiring: 173528 bytes
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 93.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 93  H   that depends on a nonexistent polymer connection! 
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.scoring.atomic_depth.AtomicDepth: actual boxlength 151, box[132*151*136], resolution  0.504

core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 31640 bytes
protocols.relax.FastRelax: CMD: endrepeat  726.868  22.7618  0.596962  0.55
core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph
core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 266 edges requiring: 173528 bytes
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 93.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 93  H   that depends on a nonexistent polymer connection! 
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.scoring.atomic_depth.AtomicDepth: actual boxlength 151, box[132*151*136], resolution  0.504

core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 31640 bytes
protocols::checkpoint: Deleting checkpoints of FastRelax
MPNN generated 1 sequences in 1 seconds
core.io.silent.SilentFileData: [ WARNING ] renamed tag lhyal_binder_9_dldesign_0_cycle0 to lhyal_binder_9_dldesign_0_cycle0_1    (SilentStruct with lhyal_binder_9_dldesign_0_cycle0 already exists!)
lhyal_binder_9 reported success. 1 designs generated in 141 seconds
Attempting pose: lhyal_pocket_0
Traceback (most recent call last):
  File "/root/autodl-tmp/dl_binder_design/mpnn_fr/dl_interface_design.py", line 256, in <module>
    main( pdb, silent_structure, mpnn_model, sfd_in, sfd_out )
  File "/root/autodl-tmp/dl_binder_design/mpnn_fr/dl_interface_design.py", line 199, in main
    dl_design( pose, pdb, silent_structure, mpnn_model, sfd_out )
  File "/root/autodl-tmp/dl_binder_design/mpnn_fr/dl_interface_design.py", line 163, in dl_design
    chains = get_chains( pose )
  File "/root/autodl-tmp/dl_binder_design/mpnn_fr/dl_interface_design.py", line 115, in get_chains
    endB = endA + pose.split_by_chain()[2].size()
IndexError