AMBER Archive (2009)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Sat May 23 2009 - 13:16:49 CDT

Hi Ross:
I did go through the tutorial 1.

I will simulate a system.
=> Lysozyme in a low ionic strength phosphate buffer (pH 7.2 , 8.3 mM)

Since lysozyme carries +8 charges, and since the buffer is dilute and almost neutral,
does it make sence =>
if i put the lysozyme into pure water model, TIP3P + 8 CL- ion for a single lysozyme ???

Thank you
Lin

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Saturday, May 23, 2009 11:10 am
Subject: RE: [AMBER] How to choose the counter ions for proteins?
To: 'AMBER Mailing List' <amber_at_ambermd.org>

> 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
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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