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Description
When docking a ligand with HOH (water molecules) using either the standard scoring function or the solvation scoring function, I obtain an SDF file containing the docked ligand, the HOH m…
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I've run into issues with the docking procedure, using codes from [here](https://github.com/asapdiscovery/asapdiscovery/blob/main/examples/docking_and_scoring.ipynb).
I was docking a new ligand into …
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### Issue summary
Hi,
I am wondering if water molecules in a protein pdb file would be sampled during gnina docking process, with refinement used only in the rescore level and not whole protein do…
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When running Uni-Mol Docking V2 via the demo.sh script on a custom protein-ligand, every part of the process seems to complete successfully, but the result file for the ligand is different than the in…
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I'm testing a dataset of ligands against the same protein. Instead of loading the same protein pdb file everytime, is there anyway to load the pdb once, and just start docking new ligand?
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Dear team,
Thank you very much for providing Open-ComBind as a command-line tool for docking pose selection. I have results from a previous docking job using GNINA with CNN-scoring. I have 10 prote…
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Hello,
I'm trying to use AutoDock-GPU to dock a protein with several thousand very short (4nt) nucleic acid strands, and I want to make sure I'm using all of my GPU's resources to get through them qu…
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hi,when running the example of reverse docking (`python predict.py -l ./reverse/ligand_1.sdf ./reverse/ligand_2.sdf -p ./reverse/receptors -o ./test -np 40 -gpu 0 -cpu 16 -bs 16 -n reverse`), I met an…
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### Issue summary
Hi, I am trying to use GNINA for docking of macrocycles. However no matter if I use autobot_lig command and after the ligand extracted from the protein, or I enter xyz coordinates e…
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Dear Maintainers,
I have a question regarding the results on the docking tasks in the Tartarus paper. Could you help me understand how the docking scores shown in Tartarus/mols_jupyter/docking.ip…