Structural relaxation bug: Several rank structures are not generated with relaxation

[teopopescu]

Dear DynamicBind maintainers,

We are running DynamicBind docking inference command across a large set of protein structures and compounds and noticed that several docking outputs do not generate all rank pdb files as expected.

When running docking without relaxation, all rank files are generated as expected. When running with relaxation, we get less than 20 rank pdb structures (see below command). We noticed that missing structures correspond to the following logs:

rm: cannot remove 'results/test_q0_30_with_relax/index0_idx_0/rank11_reverseprocess_data_list.pkl': No such file or directory

In the above, rank11 .pdb and .sdf files are missing

Command with relaxation:

python3 run_single_protein_inference.py example.pdb  ligand.csv --savings_per_complex 1  --inference_steps 1 --samples_per_complex 20 --header test_example_ligand_no_relax --device 0  --python /opt/conda/envs/dynamicbind/bin/python3 --relax_python /opt/conda/envs/relax/bin/python3

Command without relaxation:

python3 run_single_protein_inference.py example.pdb  ligand.csv --savings_per_complex 1  --inference_steps 1 --samples_per_complex 20 --header test_example_ligand_no_relax --device 0 --no_relax --python /opt/conda/envs/dynamicbind/bin/python3 --relax_python /opt/conda/envs/relax/bin/python3

We are running this on g4dn.2xlarge AWS instance with a NVIDIA T4 GPUs. CUDA drivers work as exepected as model gets transferred to GPU.

This seems to be a bug related to the relaxation module.

Any help here would be really appreciated!