normal Calcium Parameters For CG model for protein

  • Varughese
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13 years 10 months ago #372 by Varughese
My protein has 3 calcium ions in the respective binding loops and I am trying to run a CG simulation. The only parameters for Ca2+ that I can find is from the martini_v2.0_ions.itp file which is for a hydrated calcium model. Are there any Ca2+ parameters that I can use in my CG model. If not, are there any alternatives - for example, using a partial CG, restraining the loop with calcium bound etc.?

Thanks for any and all suggestions!

Jayson

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13 years 10 months ago #373 by siewert
Replied by siewert on topic Calcium Parameters For CG model for protein
Due to the standard size of the Martini CG beads (0.47 nm), small ions in Martini are considered to have their hydration shell included. This would also be the case with Ca++. However, simply taking the parameters for sodium and increasing the charge is not likely to be the best model for (hydrated) Ca++. For a more meaningful model of doubly charged ions one would need to increase the interaction between the ion and other polar compounds, especially water, substantially.

Please keep in mind that with standard Martini the description of ions is quite approximate to begin with. For a more accurate description the new polarizable Martini water model appears more suited. With this model the hydration energy of a doubly charged ion would automatically increase.

In case you really need de-hydrated ions, you could consider changing the sigma of the LJ interaction, but this would require some work. If you know where the calcium is supposed to be bound, I would simply use a harmonic bond or constraint to keep it there without bothering changing the interactions (i.e. simply take a Qd particle with charge +2).

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