Hi Valik, I do this on a regular basis for our generators here. Basically what you will need is to:
1. Generate 3D structures for the molecules (RDKit can do that) 2. Save to SDF files (again, RDKit) 3. Convert to PDBQT (I use OpenBabel: "$ obabel -isdf structures.sdf -opdbqt -Oname-.pdbqt -m") Then you'll have the files you need. Of course, you will still need to build the pdbqt file for the target and the vina_config file, but that you only need to do once. All the best, -- Gustavo Seabra. On Tue, Jun 22, 2021 at 4:08 AM Velik Velikov <welik0...@gmail.com> wrote: > Dear all, > > > > I am constructing new molecules (de novo design) that are drug-like with > RDKit. I have my molecules in SMILES now and I need to check them with > AutoDock Vina. I have never used it and I have been trying since last week > but I kind of don’t know where to go from here. > > What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or > something else? > > Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but > it didn’t work out either. I am thinking about installing Autodock Vina on > my old windows laptop now. Appreciate any help with this tool. Thanks in > advance. > > > Best, > > Velik Velikov > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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