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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Meeko does not add water molecules to some ligands #26

Closed isilkajun closed 2 years ago

isilkajun commented 2 years ago

Hi, I am working hydrated docking with a large drug library. Meeko does not add water molecules to some of these drugs. I'm attaching one of the examples. compound1068.tar.gz

diogomart commented 2 years ago

Hi, Meeko adds waters only to hydrogen bond sites (see paper). This molecule does not have H-bond sites, so no waters are added. This is a harsh approximation to reality, where water would interact strongly with the charged methylated ammoniuns, but on the other hand I don't know if there are complexes in which a water binds between the protein and a methylated ammonium.

isilkajun commented 2 years ago

I missed this information, thank you.

diogomart commented 2 years ago

You are welcome