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Hi there, I am working on reproducing the results reported in the paper on the crossdocked dataset, and was able to successfully do so when running test.py with the crossdocked_fullatom_cond and the crossdocked_ca_joint model, i.e., by running python test.py crossdocked_ca_joint.ckpt --test_dir <crossdocked_dir>/processed_noH/test/ --outdir <output_dir> --sanitize --timesteps 50 --n_nodes_bias 5
However, when I try to run the crossdocked_fullatom_joint model I get,
0%| | 0/100
[00:00<?, ?it/s]/shared/akadan/DiffSBDD/test.py:172: UserWarning: Attempt 1/10 failed with error: 'NaN detected in EGNN output'. Trying again...
...
RuntimeError: Maximum number of retries exceeded
I tried running generate_ligands.py with this same model and parameters, and noticed that this error always arises after 5 diffusion steps. Am I doing something wrong when running this model? It seems be the right parameters as specified in the paper (i.e. 50 diffusion steps with 10 resampling steps).
Thanks in advance,
Amit
The text was updated successfully, but these errors were encountered:
amitkadan
changed the title
Issue running full atom join model
Issue running full atom joint model
Oct 2, 2023
Hi there, I am working on reproducing the results reported in the paper on the crossdocked dataset, and was able to successfully do so when running
test.py
with thecrossdocked_fullatom_cond
and thecrossdocked_ca_joint
model, i.e., by runningpython test.py crossdocked_ca_joint.ckpt --test_dir <crossdocked_dir>/processed_noH/test/ --outdir <output_dir> --sanitize --timesteps 50 --n_nodes_bias 5
However, when I try to run the
crossdocked_fullatom_joint
model I get,I tried running
generate_ligands.py
with this same model and parameters, and noticed that this error always arises after 5 diffusion steps. Am I doing something wrong when running this model? It seems be the right parameters as specified in the paper (i.e. 50 diffusion steps with 10 resampling steps).Thanks in advance,
Amit
The text was updated successfully, but these errors were encountered: