Comments (3)
patrickbryant1
commented on July 30, 2024
Hi, the limit is on protein length. A statistical representation is created from the MSA and the size of this thereby doesn't matter. However, 25 sequences is probably too shallow to get good results.
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Yogesh1-11
commented on July 30, 2024
even after chopping protein length to 490 error persists. what is the
maximum protein length for umol? Also, I am using ion(
[O-]P(=O)([O-])[O-]) as ligand.
…---------------------------------------------------------------------------
XlaRuntimeError Traceback (most recent call last)
<ipython-input-6-55efa3eb56f8> <https://localhost:8080/#> in <cell
line: 10>() 8 9 #Predict
---> 10 predict(config.CONFIG, 11 MSA_FEATS, 12
LIGAND_FEATS,
------------------------------
9 frames
------------------------------
[... skipping hidden 14 frame]
/usr/local/lib/python3.10/dist-packages/jax/_src/dispatch.py
<https://localhost:8080/#> in backend_compile(backend, built_c,
options, host_callbacks) 1010 # TODO(sharadmv): remove this
fallback when all backends allow `compile` 1011 # to take in
`host_callbacks`
-> 1012 return backend.compile(built_c, compile_options=options)
1013 1014 # TODO(phawkins): update users.
XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to
allocate 8274444288 bytes.
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patrickbryant1
commented on July 30, 2024
This depends on the available RAM. Umol has no limit. I don't know what you have available in Colab, but recommend to run it locally for bigger proteins. We have not trained on phosphorylation sites.
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Related Issues (20)
- When run the 'predict.sh', how to use GPU to accelerate it HOT 1
- ValueError: operands could not be broadcast together with shapes (19,19) (2861,2861) HOT 3
- Selection of the interaction sites and pLDTT score HOT 4
- colab notebook error in prediction step HOT 7
- Docker to run it HOT 9
- Can ligand be inputted via sdf files instead of LIGAND_SMILES format? HOT 6
- Error during conda env creation HOT 1
- How to output more predicted poses HOT 2
- Some question about giant Protein HOT 1
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- Can Umol take 1 protein and 2 small molecules at the same time? HOT 1
- ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (1313,) + inhomogeneous part. HOT 1
- Error 'bash predict.sh' HOT 1
- conda enviroment problem HOT 8
- Predict ligand positions for large protein by multiple GPUs HOT 1
- [question]: Around training the model. HOT 4
- FileNotFoundError
- Colab crashes due to error in Install dependencies step HOT 1
- RecursionError: maximum recursion depth exceeded HOT 1
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