Explicit valence for atom # 219 C, 5, is greater than permitted

[wjs20]

When I run diffpack on an antibody design I generated from diffab, I get the above error and it writes nothing to disk and just exits.

This is the pdb file (just change the extension to .pdb)
output.txt

#!/usr/bin/env bash
#
#
exec python script/inference.py -c config/inference_confidence.yaml \
                           --seed 2023 \
                           --output_dir path/to/output \
                           --pdb_files $@

| ./run_example.sh output.pdb
16:45:24   Config file: /home/ws/projects/diffpack/DiffPack/config/inference_confidence.yaml
16:45:24   {'engine': {'batch_size': 32, 'gpus': [0], 'log_interval': 1000},
 'model_checkpoint': '~/scratch/trained_model/diffpack/gearnet_edge_confidence_converted.pth',
 'optimizer': {'class': 'Adam', 'lr': 0.0001},
 'task': {'class': 'ConfidencePrediction',
          'confidence_model': {'batch_norm': True,
                               'class': 'GearNet',
                               'concat_hidden': True,
                               'edge_input_dim': 58,
                               'hidden_dims': [128, 128, 128, 128, 128, 128],
                               'input_dim': 39,
                               'num_angle_bin': 8,
                               'num_relation': 6,
                               'readout': 'sum',
                               'short_cut': True},
          'graph_construction_model': {'class': 'GraphConstruction',
                                       'edge_feature': 'gearnet',
                                       'edge_layers': [{'class': 'BondEdge'},
                                                       {'class': 'SpatialEdge',
                                                        'min_distance': 2,
                                                        'radius': 4.5},
                                                       {'class': 'KNNEdge',
                                                        'k': 10,
                                                        'min_distance': 0}]},
          'model': {'batch_norm': True,
                    'class': 'GearNet',
                    'concat_hidden': True,
                    'edge_input_dim': 58,
                    'hidden_dims': [128, 128, 128, 128, 128, 128],
                    'input_dim': 128,
                    'num_angle_bin': 8,
                    'num_relation': 6,
                    'readout': 'sum',
                    'short_cut': True},
          'num_mlp_layer': 3,
          'num_sample': 4,
          'schedule_1pi_periodic': {'annealed_temp': 3,
                                    'cache_folder': '~/scratch/output/diffpack',
                                    'class': 'SO2VESchedule',
                                    'mode': 'ode',
                                    'pi_periodic': True},
          'schedule_2pi_periodic': {'annealed_temp': 3,
                                    'cache_folder': '~/scratch/output/diffpack',
                                    'class': 'SO2VESchedule',
                                    'mode': 'ode',
                                    'pi_periodic': False},
          'sigma_embedding': {'class': 'SigmaEmbeddingLayer',
                              'hidden_dims': [64, 128],
                              'input_dim': 39,
                              'sigma_dim': 64},
          'torsion_mlp_hidden_dims': [64, 128],
          'train_chi_id': None},
 'test_set': {'atom_feature': 'residue_symbol',
              'bond_feature': None,
              'class': 'SideChainDataset',
              'mol_feature': None,
              'path': None,
              'pdb_files': ['output_test.pdb'],
              'removeHs': True,
              'residue_feature': None,
              'sanitize': True,
              'transform': {'class': 'Compose', 'transforms': []}},
 'train': {'num_epoch': 0}}
16:45:24   Output dir: /home/ws/projects/diffpack/DiffPack/path/to/output
16:45:34   Preprocess training set
16:45:37   {'batch_size': 32,
 'class': 'core.Engine',
 'gpus': [0],
 'gradient_interval': 1,
 'log_interval': 1000,
 'logger': 'logging',
 'num_worker': 0,
 'optimizer': None,
 'scheduler': None,
 'task': {'class': 'tasks.ConfidencePrediction',
          'graph_construction_model': {'class': 'layers.GraphConstruction',
                                       'edge_feature': 'gearnet',
                                       'edge_layers': [{'class': 'layers.geometry.BondEdge'},
                                                       {'class': 'layers.geometry.SpatialEdge',
                                                        'max_distance': None,
                                                        'max_num_neighbors': 32,
                                                        'min_distance': 2,
                                                        'radius': 4.5},
                                                       {'class': 'layers.geometry.KNNEdge',
                                                        'k': 10,
                                                        'max_distance': None,
                                                        'min_distance': 0}],
                                       'node_layers': None},
          'model': {'activation': 'relu',
                    'batch_norm': True,
                    'class': 'models.GearNet',
                    'concat_hidden': True,
                    'edge_input_dim': 58,
                    'hidden_dims': [128, 128, 128, 128, 128, 128],
                    'input_dim': 128,
                    'num_angle_bin': 8,
                    'num_relation': 6,
                    'readout': 'sum',
                    'short_cut': True},
          'schedule_1pi_periodic': {'PI': 1.5707963267948966,
                                    'cache_folder': '~/scratch/output/diffpack',
                                    'class': 'SO2VESchedule'},
          'schedule_2pi_periodic': {'PI': 3.141592653589793,
                                    'cache_folder': '~/scratch/output/diffpack',
                                    'class': 'SO2VESchedule'},
          'sigma_embedding': {'class': 'layers.SigmaEmbeddingLayer',
                              'embed_type': 'sinusoidal',
                              'hidden_dims': [64, 128],
                              'input_dim': 39,
                              'operation': 'post_add',
                              'sigma_dim': 64},
          'torsion_mlp_hidden_dims': [64, 128],
          'train_chi_id': None,
          'verbose': 0},
 'test_set': None,
 'train_set': None,
 'valid_set': None}
16:45:37   #parameter: 9351987
16:45:37   Loading dataset from pdb files
Constructing proteins from pdbs:   0%|                                                                                                                                                                                | 0/1 [00:00<?, ?it/s][16:45:37] Explicit valence for atom # 219 C, 5, is greater than permitted
Constructing proteins from pdbs: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00,  9.68it/s]
16:45:37   Test on SideChainDataset(  #sample: 0)
16:45:37   /home/ws/projects/diffpack/DiffPack/path/to/output