I want to dock Silver nanoparticles with a protein, but there is no parameter for Silver. any idea to parametrize Silver?
Following Parameters are required for AutoDock.. # - 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) # - solpar = atomic solvation parameter # - Rij_hb = H-bond radius of the heteroatom in contact with a hydrogen (in Angstrom) # - epsij_hb = well depth of H-bond (in Kcal/mol) # - hbond = integer indicating type of H-bonding atom (0=no H-bond) # - rec_index = initialised to -1, but later on holds count of how many of this atom type are in receptor # - map_index = initialised to -1, but later on holds the index of the AutoGrid map # - bond_index = used in AutoDock to detect bonds; see "mdist.h", enum {C,N,O,H,XX,P,S}
Dear Shahzad,
Hopefully the following link will help you in resolving your issue
http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html.
from there I got following parameter for Ag, you can try with
atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
Best of luck
Here It is
atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
thanks brother but i had already found this.. Actually i want to do this by my own, is it possible??
I don't know if i get it but, you can modify these parameters as you wish, then add it to your forcefield parameter file. You can use element parameters provided in literature, if you want, you can follow a parametrization protocol
Please see
Computational Organometallic Chemistry with Force Fields Jing Huang, Michael Devereux, Franziska Hofmann, and Markus Meuwly
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