ab_opt

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Error while executing optimize_ab.py in 7DK2_AB_C.pdb

4

Hello, I was following the "Pratope-epitope Docking using AbDock" pipeline inside the AbDock folder. When executing the script optimize_ab.py, the following error came up: $ python optimize_ab.py --num_gpus 1 --process_per_gpu...

dealmeida-vm

Error while training

3

File "./ab_opt/AbDesign/diffab/models/diff_gnn.py", line 149, in forward hydropathy = batch['hydropathy'][batch['mask']] KeyError: 'hydropathy' also with 'charge' key

Melissaurious

How to use AbDock without Ag-Ab complex?

1

Thank you for the execellent work! If I only have the PDB files for the antigen and antibody structures separately, and not the combined structure of the antigen-antibody complex, how...

Hyeongsun

AbDesign error while evaluating.

2

Hi, thanks for excellent work! I encounted an error when running code 'python design_testset.py', how can I fix it? ``` Traceback (most recent call last): File "/home/disk02/ab_design/miniconda3/envs/diffab/lib/python3.8/site-packages/pandas/core/nanops.py", line 1680, in...

Thoudam-A

python dock_pdb.py --pdb_path data/examples/7DK2_AB_C.pdb Report this error as follow: [INFO] Renumbered chain A (H) [INFO] Renumbered chain B (K) [INFO] Chain C does not contain valid Fv: Variable chain sequence...

Jubird915

ab_opt.ipynb: name 'res' is not defined

2

Hello! Thank your for your amazing work! During the execution of the first block of the code, an error 'name 'res' is not defined' occurred. How can I fixed it?

adriansh11

Does optimize_ab.py support multiple CDRs?

3

Hello, Could you suggest a way to optimize multiple CDRs? I've tried two options, but I need help to get them to work. 1. --design_contig "95-102" 2. (all) ``` File...

TangYiChing

Whole structure/sequence modified during despite training only on codesign_single_gnn

1

Hello! I used the training and inference scripts and configurations provided, however, when I analyze my results I see that even that the reference and the mutant structure almost overlap,...

Melissaurious

Hi, thanks for excellent work! I ran command like this: python design_pdb.py ./data/examples/8X0Y_complex.pdb --config ./configs/test/codesign_single.yml and encountered an error, the result is: --- ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in...

Thoudam-A