Based on PubChem calculation, the ligand structure only possess 1 rotational bond (TORSDOF). However, the ligand structure that came out from DFT optimization has been calculated differently by AutoDock with 5 TORSDOF. Interestingly, from 5 of them, there is not any single bond that the same one as what PubChem found.
So, should I directly just use DFT-optimized ligand structure OR I change the TORSDOF number and rewrite its structure file (.pdbqt), then use the rewrited one?
Christian Kenneth, you can use optimised structures for docking. Those structures will be having more stability. You can even prepare the ligands by importing the structures in which you will get more conformers. For analysis purpose you can use one DFT optimised structure.
If there is a bias to the initial geometry of the ligand, and if the bias is undesirable, consider changing the molecular docking program. There are docking algorithms not biased to the initial geometry of the ligand (e.g., FlexX).
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