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dauparas / LigandMPNN

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Designing HOMO-OLIGOMER error #10

Open Lyang556 opened 8 months ago

Lyang556 commented 8 months ago

@dauparas Thanks for you hard work. I think I found a bug. My command is:

python run.py \ --fixed_residues "A51 A52 A53 B154 B155 B156 C257 C258 C259 D360 D361 D362 E463 E464 E465 F566 F567 F568" ` --pdb_path "./design_4.pdb" ` --out_folder "./outputs/test" ` --batch_size 3 ` --number_of_batches 5 ` --temperature 0.1 ` --homo_oligomer 1`

The error is: Designing HOMO-OLIGOMER Traceback (most recent call last): File "DL_biosoft/LigandMPNN/run.py", line 794, in <module> main(args) File "DL_biosoft/LigandMPNN/run.py", line 315, in main tmp_list.append(encoded_residue_dict[name]) ~~~~~~~~~~~~~~~~~~~~^^^^^^ KeyError: 'A310' ` Could you please help me solve this error? The PDB file is attached。 design_4.zip

Thank you.

Lyang556 commented 8 months ago

I've solved this issue by renumbering the PDB files using the "pdb_renumber.py" script in rosetta. Could you please tell me if there are any other possible ways to solve this issue? Thanks you.