Error in running inference_single.py

[kdinashi]

When trying to run inference_single.py on two pdb files, I get the following error:

line 515, in inference
model = DFMDock.load_from_checkpoint(
............
raise ConfigKeyError(f"Missing key {key!s}")
omegaconf.errors.ConfigAttributeError: Missing key crop_size
full_key: crop_size
object_type=dict

Could you help me resolve this error?

[lchu11]

Just edited. Let me know if it works. Thanks!

[kdinashi]

Thank you for the update. Now the error has changed:

Traceback (most recent call last):
File "/home/kimia/DFMDock/src/inference_single.py", line 12, in
inference(args.pdb_1, args.pdb_2)
File "/home/kimia/DFMDock/src/inference_base.py", line 645, in inference
rec_pos, lig_pos, rot_update, tr_update, outputs = Euler_Maruyama_sampler(
File "/home/kimia/DFMDock/src/inference_base.py", line 426, in Euler_Maruyama_sampler
output = model(batch)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/home/kimia/DFMDock/src/models/score_model_mlsb.py", line 62, in forward
outputs = self.net(batch, predict=True)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/home/kimia/DFMDock/src/models/score_net_mlsb.py", line 370, in forward
edge = self.spatial_embed(spatial_matrix) + self.positional_embed(position_matrix)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
return forward_call(*args, **kwargs)
File "/home/kimia/miniconda3/envs/DFMDock/lib/python3.10/site-packages/torch/nn/modules/linear.py", line 117, in forward
return F.linear(input, self.weight, self.bias)
RuntimeError: mat1 and mat2 shapes cannot be multiplied (204304x66 and 67x128)

I appreciate your assistance!