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

[Zhenting Gao]

Hi Maciek,


Thanks for providing the ODDT solution.
I need some examples and documents to learn ODDT. Where could I find them?


Regards
Zhenting


------------------ 原始邮件 ------------------
发件人:&nbsp;"Maciek Wójcikowski"<mac...@wojcikowski.pl&gt;;
发送时间:&nbsp;2020年4月11日(星期六) 晚上10:30
收件人:&nbsp;"Zhenting Gao"<183310...@qq.com&gt;;
抄送:&nbsp;"Rdkit-discuss"<rdkit-discuss@lists.sourceforge.net&gt;;
主题:&nbsp;Re: [Rdkit-discuss] Can we use Rdkit to generate pdbqt file for 
AutoDock Vina?



Hi Zhenting,

RDKit does not have PDBTQ writer as you mentioned, but I have implemented one 
in 
ODDT&nbsp;https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.MolToPDBQTBlock


I also can warn you that reading back molecules from PDBQT might mess up your 
bond orders.


In ODDT it is also possible to run a docking "pipeline" with Vina using RDKit 
exclusively, and use SDFs as a input/output.


----
Pozdrawiam, &nbsp;| &nbsp;Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl






sob., 11 kwi 2020 o 15:57&nbsp;Zhenting Gao <183310...@qq.com&gt; napisał(a):

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




------------------&nbsp;Original&nbsp;------------------
From:&nbsp;"我自己的邮箱"<183310...@qq.com&gt;;
Date:&nbsp;Fri, Apr 10, 2020 12:35 PM
To:&nbsp;"Rdkit-discuss"<rdkit-discuss@lists.sourceforge.net&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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