AMBER Archive (2009)

Subject: RE: [AMBER] How to choose the counter ions for proteins?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat May 23 2009 - 13:09:27 CDT

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 |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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