I want to perform Molecular dynamic simulations of metalloprotein containing cadmium ion. To treat metal ions, there are different force field available, how can we decide which force field is appropriate for a particular metal ion?
Hi Anu,
You should check the following links:
http://ambermd.org/
http://ambermd.org/tutorials/
http://ambermd.org/tutorials/advanced/tutorial20/
An excellent paper has been published in the nature regarding your question by Kevin J. Waldron1, Julian C. Rutherford, Dianne Ford & Nigel J. Robinson as follows:
Nature 460, 823-830 (13 August 2009) | doi:10.1038/nature08300; Published online 12 August 2009
It might be useful for you
Dear Anu,
Simulate metals (in general) by MD simulations is a real challenge! Consider yourself that a metal in classical force fields is a point integer fixed charge and a pair of Lennard-Jones parameters...saying this, and far as I know, we can not simulate at the same time the water-exchange (that is an energetic term), the coordination geometry and ion-oxygen distance that define the chemistry of a metal! you must choose to sacrifice one parameter depending of your needs.
Please see our paper about this, in our case we performed classical TI simulations to find the best L-J parameters....but it was a hard work!!!
https://www.researchgate.net/publication/269407762_Helix-Coil_Transition_Induced_by_Metal_Ion_Interaction_with_a_Grafted_Iron-Binding_Site_of_the_CyaY_Protein_Family
Article Helix–Coil Transition Induced by Metal Ion Interaction with ...
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