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Designing HOMO-OLIGOMER error #10

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Lyang556 opened this issue Mar 13, 2024 · 1 comment
Open

Designing HOMO-OLIGOMER error #10

Lyang556 opened this issue Mar 13, 2024 · 1 comment

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@Lyang556
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@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
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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.

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