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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Problem about prepared ligand hydrogen #49

Closed FeiLiuEM closed 11 months ago

FeiLiuEM commented 1 year ago

Hello,

I have a problem about mk_prepare_ligand.py.

I use mk_prepare_ligand.py -i ligand.sdf -o ligand.pdbqt to prepare ligand. However, when I open ligand.pdbqt by pymol. I find that it could use h_add to add hydrogen for the pdbqt file.

I don't know why it happens. So, I have 2 questions:

  1. Is this because I didn't add keep_nonpolar_hydrogens=True?
  2. Does it affect the outcome of docking?
diogomart commented 1 year ago

Hello, the PDBQT are supposed to have only polar hydrogens, which are those bound to oxygen and nitrogen for most molecules. If you are missing those hydrogens, it's a problem. Non-polar hydrogens (e.g. bound to carbon) should not be there.

FeiLiuEM commented 1 year ago

Thank you diogomart! @diogomart

You solved big problems for me.

Thanks ever so.