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
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