[gmx-users] Modeling a nickel binding site
Mark.Abraham at anu.edu.au
Tue Dec 9 06:31:33 CET 2008
> 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.
More information about the gromacs.org_gmx-users