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
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