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In the PDBbind2016 data directory, I see the following files that seems to be used in your training project.
<PDBid>_nowat.pdb -- Receptor structure with all HETATOMS removed
I was wondering how to generate thenowat.pdb
forpocket.pdb
files in PDBbind 2019 dataset, and the ChatGPT told me to use:
for file in *.pdb; do gnina -i "$file" -o "${file%.pdb}_nowat.pdb" --autobox_ligand ""; done
I am not sure if this is the same way of your project. If so, even though it works, it might have some differences with your dataset. So I am here to ask your methods to generate 'nowat.pdb' in details.
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