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Hi,
Since I am done with the initial port of hh-suite to ppc64le and that I am able to run a few commands mentioned in the User Guide without crashing hh-suite, I am looking for testing the ported …
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Hi,
We are trying to install alphafold on a cluster, where we do not have sudo privileges nor are we allowed to use docker.
Hence, we are following the setup that can be found here: https://github…
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I am having a recurrent problem when trying to use hhblits. It runs to a certain point then fails with this message: Segmentation fault (core dumped). I noticed this usually occurs right after the HMM…
lwadi updated
2 years ago
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I have installed alphafold2 using the non-docker method on HPC, I am running the script using GPU (V100 with 16 GB of memory).
For a sequence of around 200 amino acids, It is taking around 8 hours fo…
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Hi,
i am running the latest release of fastfold using this command:
```
python inference.py input.fa database/pdb_mmcif/mmcif_files/ \
--output_dir output/ \
--gpus 1 \
--model_pr…
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We have TMAlign/APoc results files (whether parsed or not). Need to pull the PDB IDs associated with top hits, grab the respective UniProt IDs. With a UniProt ID, we need to gather the metadata file f…
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Hi Patrick,
The test sample ran perfectly but I received this error when trying on my sample
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Hello,
is there a way to run alphafold in a cluster environment with a job scheduling system (slurm/openpbs)?
I have several nodes with strong GPUs available, I would like to use them as well.
…
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I see
```
(RF2) [kimd999@tlogin3 examples]$ ../run_RF2.sh rcsb_pdb_7UGF.fasta -o 7UGF_by_tmux
Running HHblits
-> Running command: /home/kimd999/script/python/RoseTTAFold2/input_prep/make_prot…
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```
Traceback (most recent call last):
File "run_alphafold.py", line 338, in
app.run(main)
File "/home/yulab/anaconda3/envs/af2/lib/python3.8/site-packages/absl/app.py", line 312, in run
…