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Docking of gold nanoparticles using autodock
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Author:  mshahbaaz [ Thu Feb 16, 2017 9:33 pm ]
Post subject:  Docking of gold nanoparticles using autodock


How are you

I am trying to dock the gold nanoparticles to the protein. I am able to form the nano.pdbqt file. But When I am running the docking simulation. Th following error occurred.

unknown ligand atom type Au
add parameters for it to the parameter library first!

I tried to add the parameters to this file. But I dont know the exact parameters for Au.
These are

Rii = sum of vdW radii of two like atoms (in Angstrom)
epsii = vdW well depth (in Kcal/mol)
vol = atomic solvation volume (in Angstrom^3) (4/3*pi*(Rii/2)**3)
solpar = atomic solvation parameter

Can any body tell me these parameters for Au or how to calculate these parameters for Au. Then I can able to run the docking Thanks


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