I am trying to perform a docking between my enzyme and the substrate using AutoDock Vina but the output of the program is a strucutre with atoms bond even when they are far, unnatural torsions... Does anyone know how can I fix this?
Thank you!
Unnatural bond? can you describe more? If the docking not reflex or mimic what in the lab/crystal structure, there are a lot of possibility.
1) Preparation protein such as protonation state, missing atom and residues, energy minimize,
2) Preparation of ligand/substrate such as, it is already in energy minimize, are the hydrogen mimic what it should be,
3) Parameter setting such as box size and coordinate, how you do that, did you include all the important residues in the box
4) Control docking - you needs to test for other know inhibitor and inactive compounds
I know there are a lot of work need to be done and careful if you have histidine in the box because AD tool will set the histidine protonated as default, so this also might lead to unnatural bond. So good luck for your work...
Thank you all for your suggestions. The problem was on the structure of the ligand and no in the docking.
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