Thank you Jesper for suggesting the following two articles
http://dx.doi.org/10.1016/j.jmb.2006.10.095 and
http://dx.doi.org/10.1021/ct400177g , which discussed relevant issues in simulating systems with metal ions. Specifically the "J. Mol. Biol. (2007) 366, 687-701" article used a MD62+ model and is applied to a binuclear site with two Mg2+ ions similar to my case. However, I need guidance with setting up such a system. Is there any help available in amber in setting up such models? Also, I am not sure if I have to use such a model to prevent repulsion between the two Mg2+ ions or a simpler distance/position restraints will be sufficient?
Thanks and regards,
Latha.
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Received on Wed Aug 14 2013 - 16:00:03 PDT
