[gmx-users] Modeling a nickel binding site

Xia,Wei weixia1984 at gmail.com
Tue Dec 9 05:55:35 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?
I would appreciate your help!

Wei Xia

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