[gmx-users] metal_ligand complex

[tarak karmakar]

Dear All,


In my system, I want to see the binding of a ligand, composed of a
divalent metal and 6 ligands, to a protein. I am not sure that
movement of this type of complex ( ligand) towards the protein active
site cavity can be feasible or not.  If anyone has some experience or
idea for this kind of problem, please describe me in brief.

Should we assign charges of the metal ions as they have their own or
 in presence of  ligands ( mainly negative charges) , reduced charges ??

Thanks

-- 
Tarak