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NiBoyang / AutoDock-SS

Use AutoDock for Ligand-based Virtual Screening
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Git LFS Bandwidth Out #3

Open cmwilson252 opened 2 months ago

cmwilson252 commented 2 months ago

When pulling the data set using git lfs pull I run into the following error:

batch response: This repository is over its data quota. Account responsible for LFS bandwidth should purchase more data packs to restore access. error: failed to fetch some objects from 'https://github.com/NiBoyang/AutoDock-SS.git/info/lfs'

NiBoyang commented 2 months ago

Hi @cmwilson252 , it seems that too many pulls have used all my data quota and I have to pay 10 dollars/m to GitHub for additional quota. May I know which data set do you want and so that I can send it to you via a link.

cmwilson252 commented 2 months ago

Hello, I would like any dataset that includes a pdbqt and sdf files that successfully dock to the pdbqt. Do you guys have a good method to translate pdbs without connect records to pdbqts?

cmwilson252 commented 2 months ago

Hello @NiBoyang do you have any update on this?

NiBoyang commented 2 months ago

Hi @cmwilson252 Sorry for the late reply as I'm a bit busy with my new project. I attached a target from DUD-E with a prepared pdbqt file and libraries in sdf.gz. abl1.zip

Re. translating pdbs to pdbqts without connect records, if you check the ligandprep.py (which is a python3 version of prepare_ligand4.py in the AutoDockTool), the line 41 says print(" [-Z] inactivate all active torsions "). So calling with -Z should deactivate all torsions.