Re: [AMBER] adding hydrogen to pdbqt ligand files

From: Eduardo Mayo <>
Date: Fri, 29 May 2020 02:25:00 -0400

I recommend:
1 convert to .mol file using babel (with and without -h) and check if the
tautomeric state is the desired.
2 if 1 didn't work then covert to smarts or smiles( so if you got a
tautomeric state with local charge the smarts/smiles will have this
information) . Use rdkit to covert smiles/smarts to rdkit.Mol and add then
the hydrogen. Chem.Embedded the molecule so you have a 3D model. The read
the mol file using Chem.MolFromMolFile. Align (you may need find the mcse)
the molecule obtained from smiles to the molecule obtained from the mol

Message: 3
Date: Tue, 28 Apr 2020 21:15:36 +0000 (UTC)
From: Marawan Hussien <>
Subject: [AMBER] adding hydrogen to pdbqt ligand files
To: AMBER Mailing List <>
Message-ID: <>
Content-Type: text/plain; charset=UTF-8

 Is there is a standard leap command to add hydrogen atoms to non-polar
atoms (carbons) only during system building? I am preparing a
protein-ligand system for MD from pdbqt protein-ligand complex and do not
want to change the ligand tautomeric state.? I tried rdkit, obabel, chimera
but every tool I tried will add hydrogen to the entire molecule, not carbon
atoms only? Any suggestion?
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Received on Thu May 28 2020 - 23:30:02 PDT
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