[gmx-users] Modeling a nickel binding site

[Mark Abraham]

Xia,Wei wrote:
> Dear All:
> Could anyone give me an example how to introduce a nickel ion into a 
> protein simulation.
> I have got a apo-form protein structure and know the approximate 
> coordination for the nickel
> ion. What I want to do is to run a energy minimization to make the 
> nickel ion in place.
> However, in the apo-form structure the nickel binding ligands are too 
> far away from each other.
> Is it possible to ‘pull' them together during the energy minimization?

This is one of the purposes for "distance restraints". Please read the 
relevant section in Chapter 4 of the manual, and much of Chapter 5.

Mark