[gmx-users] Modeling a nickel binding site

[Xia,Wei]

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?
I would appreciate your help!
Best!

Wei Xia