Storage requirement

[ryupath]

I'm wondering how many GB of storage do I need to run the script.
To calculate the structures of one ligand and 1100 receptors, like in the article, I'm now using HPC system. If the storage exceeds 1TB, I need to have additional paperwork to use the system. Please tell me.

[denizkavi]

The databases needed for MSA will be larger than 1 TB. From the AlphaFold repository:

Note: The total download size for the full databases is around 556 GB and the total size when unzipped is 2.62 TB. Please make sure you have a large enough hard drive space, bandwidth and time to download. We recommend using an SSD for better genetic search performance.

This repo uses a reduced version of bfd, but the total is most likely still larger than 1 TB to have the whole of the databases. If this is not feasible, you might try using localcolabfold , which does the MSA step in an external server.

[ryupath]

To denizkavi
Thank you for your kind response. The DB is installed in shared disc space in the HPC system. So I do not have to install it in my own disc space.

I want to know how many GB of files(MSA, pkl, .pdb files, etc.) does it produce if I run the script with fasta files of one ligand and 1100 receptors.

[denizkavi]

It's pretty unlikely that 1100 total predictions will produce files exceeding 1 TB in size.

[ryupath]

How did you deal with a protein such as Q9H7V2 which have two extracellular domains. There are several proteins like this.