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Hello!
I tried to convert a pdb file to pdbqt and then I will achieve some task of docking (with Autodock Vina). But a warning occurred:
*** Open Babel Warning in PerceiveBondOrders
Failed …
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has anyone been able to get --flex or flexible residues in the receptor to work? Or are they interested?
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Hi All,
My protein contains a Ni metal. I thought the parameter file was the parameter files in AutoDock-Vina/data AD4Zn.dat vs AD4_parameters.dat so i put Ni into those files. However, im …
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### Issue summary
Hi
May I ask what empirical scoring functions are used in the Monte Carlo chain, the refinement after the aggregating the top poses from each MC chain, and the final step?
…
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Thanks for your interesting work!
Can you provide more details about the docking protocols of the molecular docking software mentioned in your paper (e.g. Autodock Vina, Vinardo, Smina)? I would like…
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https://www.biodasturchi.uz/posts/2022-09-29-ligand-docking-and-binding-site-analysis.html
Docking of various therapeutically important chemical entities to the specific target sites...
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Thanks for your great efforts on enlarging the atom num and size of grid boxes. However I encountered errors
> ' Err-4:CL_MEM_OBJECT_ALLOCATION_FAILURE'
when using AutoDock-GPU-Vina-2.1 run th…
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I'm following the Flexible Docking tutorial found here: [https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html](https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html) on …
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I prepared a PDB file with a structure of beta-cyclodextrin (BCD.pdb), based on crystallographic data. Beta-cyclodextrin is a cyclic macromolecule, consisting of seven linked glucose residues. I woul…
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Hello,
I have used AutoDock-vina (vina scoring function) for docking a ligand inside a target which I have the experimental result. The docking result is not aligned with the experimental result even…