Hi
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
Regards
Hi,
atom_par Au 3.29 0.039 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
see the attachment.
But Mohd S, I wonder how you have been able to build Au nanoparticals and how you assigned computed the charges? I would like to hear from you if you succeed in such type of docking. This is because, I tried to build solid lipid nanoparticles entrapping tamoxifen and docking it against one protein, but failed.
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