Hi Zhenting, RDKit does not have PDBTQ writer as you mentioned, but I have implemented one in ODDT 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, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl sob., 11 kwi 2020 o 15:57 Zhenting Gao <183310...@qq.com> 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 > > > ------------------ Original ------------------ > *From:* "我自己的邮箱"<183310...@qq.com>; > *Date:* Fri, Apr 10, 2020 12:35 PM > *To:* "Rdkit-discuss"<rdkit-discuss@lists.sourceforge.net>; > *Subject:* 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 > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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