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Error running cremdock script #66

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DrrDom opened this issue Feb 10, 2025 · 5 comments
Open

Error running cremdock script #66

DrrDom opened this issue Feb 10, 2025 · 5 comments

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@DrrDom
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DrrDom commented Feb 10, 2025

The original issue DrrDom/crem#33

This is the command I entered:
% cremdock -i input.smi -o mode1_1.db -d chembl22_sa2_hac12.db --nclust 2 --max_replacements 2 --program vina --confi vina_config.yml -c 2

And the error I am facing:

/Users/vipraparekh/anaconda3/envs/thesis/lib/python3.9/site-packages/prolif/datafiles.py:3: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import resource_filename
Traceback (most recent call last):
File "/Users/vipraparekh/anaconda3/envs/thesis/bin/cremdock", line 8, in
sys.exit(entry_point())
File "/Users/vipraparekh/anaconda3/envs/thesis/lib/python3.9/site-packages/cremdock/cremdock.py", line 282, in entry_point
args_dict, tmpfiles = eadb.restore_setup_from_db(args.output)
File "/Users/vipraparekh/anaconda3/envs/thesis/lib/python3.9/site-packages/easydock/database.py", line 105, in restore_setup_from_db
values = [v for v in res][0]
IndexError: list index out of range

@DrrDom
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DrrDom commented Feb 10, 2025

Did you remove output database after the first unsuccessful run?

@28vipraparekh
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No I did not try that.I will try that and get back to you.

@28vipraparekh
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This is the error i am facing now:

from pkg_resources import resource_filename
/Users/vipraparekh/anaconda3/envs/thesis/lib/python3.9/site-packages/prolif/datafiles.py:3: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html

And this error is being displayed on loop multiple times

@DrrDom
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DrrDom commented Feb 10, 2025

This is a warning, not an error. So, I guess the generation runs fine.
To track progress you may look inside the output database or in the log file.

@28vipraparekh
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Okay
Thank you so much for your prompt response and help.

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