johnny-rodriguez

Does CUDA version matter?

3

I checked if Alphafold can use the GPU by running the following: docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi I get the following error: Unable to find image 'nvidia/cuda:11.0-base' locally...

I am running the following colabfold command: colabfold_batch \ --num-recycle 3 \ --msa-mode single_sequence \ --amber \ --use-gpu-relax \ --num-relax 1 \ --num-model 2 \ --model-order 1,2 \ --templates \...

MSA generation failed

1

I am having trouble running the generate_msas.sh. script. I see some errors with certain packages. Can you recommend a fix? /home/johnny/Documents/AFProfile/data/test/test.fasta /home/johnny/.local/lib/python3.10/site-packages/Bio/Data/SCOPData.py:18: BiopythonDeprecationWarning: The 'Bio.Data.SCOPData' module will be deprecated in...

I have downloaded the AF2 multimer and Openfold soloseq model weights. I am unable to find the openfold multimer model weights. Have the been released? If so, where do I...

To make my filenames cleaner, I want to know where in the code I can change how the output colab batch files are named. Thanks