I'm trying to run a simulation with a protein and a Ca2+ Ion but I have a few questions: what is the better software to run the simulation? Does a tutorial exist that shows a few directions because it is different running a simple dock?
I do not know if understood well, but if you mean that you want to run a molecular dynamics simulation of a protein that contains a bound Ca2+ ion, most forcefields (ie. OPLS, AMBER,...) should have parameters for it. You can try MD packages such as Gromacs or NAMD, which are free for academics, with any of those forcefields. On the other hand, if you want to dock some small organic molecules to a protein that contains a bound calcium in the bindig site, this should also be possible with many packages. Autodock, for example, has parameters for calcium (http://autodock.scripps.edu/resources/parameters/AD4.1_bound.dat/view), or Glide, which uses OPLS, is another option, although it is a commercial package. About tutorials, I think that you will find info on the documentation of both packages, although dealing with metal ions is mostly a matter of considering them as part of the receptor (as long as there are appropriate parameters for them) and that your ligands are in the right state (ionization, tautomers,...) for coordination if that should contribute to binding.
I Will suggest you to run either Gromacs4.6 or Amber. I have done with gromacs and got good result. You can try it..its good and easy...Here for your comfort i am attaching the tutorial for latest gromacs.
The main inconvenient in running such kind of MD is the cation mobility. For that reason, I strongly recomend to you to make use of restraint methods during your simulation to freeze the cation position.
There are so many good MD packages for doing so (Amber, NAMD, Gromacs) but in any case, the above-mentioned restraint deployment is mandatory in order to preserve the cation-protein interaction.
Best regards
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