Comments (4)
Hi Junhui,
This file should be copied over during the Docker build process as given in the Dockerfile:
https://github.com/deepmind/alphafold/blob/main/docker/Dockerfile#L60-L61
Is that not working?
(If you are setting up without using Docker I recommend following the Dockerfile to make sure you get all the steps and correct versions.)
from alphafold.
Oh, I was running it on a non docker cluster using the script run_alphafold.py
(since our HPC doesn't and will not support Docker container...). Thanks for clarifying!
from alphafold.
No problem! I believe there are some other issues discussing how to run it without Docker, if that helps.
from alphafold.
I had a similar problem on a non_docker install.
I noticed that the file failed to download due to a certificate error reported by wget. The command indicated on the website uses the -q
option. This option prevented the error from being reported.
The command for "Download chemical properties to the common folder" is indicated on the website:
wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
I just removed the -q
and used --no-check-certificate
. This solved my case:
wget --no-check-certificate -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
from alphafold.
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