Re: [Rdkit-discuss] Can we use Rdkit to generate pdbqt file for AutoDock Vina?

Sat, 11 Apr 2020 06:57:48 -0700 

Hi,


I've got a solution now.
Here are the keys:
1. OpenBabel can convert SDF to PDBQT. During conversion, non-polar hydrogen 
will be removed.
2. OpenBabel can assign Gasteiger charge to molecule. Although the assigned 
charge is different from OpenBable and AutoDockTools, AutoDock Vina will omit 
the charges in input file.


HTH
Zhenting




------------------ Original ------------------
From:&nbsp;"????????????"<[email protected]&gt;;
Date:&nbsp;Fri, Apr 10, 2020 12:35 PM
To:&nbsp;"Rdkit-discuss"<[email protected]&gt;;

Subject:&nbsp;Can we use Rdkit to generate pdbqt file for AutoDock Vina?



Hi there,

Regarding to open-source CADD tools, Rdkit and AutoDock are really essential.
Can we use Rdkit to generate pdbqt file for AutoDock Vina?
Please also inform if you have solutions other than Rdkit.


I am trying to leverage the MGLtoos now.


Best regards
Zhenting
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