Modelling Electrostatic Interactions
Scoring and Minimization with AutoDock Vina
Status: Beta
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Hello,
I was browsing other posts that people have brought up and learned that the vinardo default scoring function does not take into account partial charges. I want to model a protein-ligand interaction that centers around a asparagine + lysine catalytic domain (positive charge) that interacts with a carboxylate group (negative). What is the best way to model this? I'm thinking of either changing some parameters for the nitrogen atom, or changing the weight of nitrogen oxygen atom pairs? Any thought would be greatly appreciated!
The hydrogen bond term of the default Vina scoring will capture that interaction just fine, but you can create a custom scoring function with a Coulomb electrostatic potential if you'd prefer or using the ad4_scoring option which has an electrostatic term.
Got it. Thanks! Also sorry to bother you but one other question I had was when calling the --score_only, what does the intramolecular energy output measure? Is it the energy of the binding or is it the binding of the ligand, the receptor, etc? Thanks so much again!
Intramolecular energy is from the ligand interacting with itself.
Ah I see. Thank you!