Hi Lin,
> How to choose the counter ions for proteins?
> Proteins are made of amino acids.
> Does it mean the counter ions of protein H+ or OH-?
> Does amber have the default ions of H+ and OH-?
I think one could argue that this should perhaps be H3O+ to represent H+
ions in solution. However, typically one does not use pure water in
experiment but often buffered solutions. In simulation one typically
neutralizes using Na+, K+ or Cl- ions. I suggest taking a look at the first
tutorial:
http://ambermd.org/tutorials/basic/tutorial1/
This gives an example of including counter ions in a simulation.
Good luck,
Ross
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Sun May 24 2009 - 01:10:54 PDT
