AMBER Archive (2009)

Subject: Re: [AMBER] Why NaCl or KCl solution?

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed May 27 2009 - 21:11:21 CDT

Hi
I am going to simulate the lysozyme with some ligand in the low ionic strength phosphate buffer .

The buffer condition will be
(pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM)

For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water model and use CL- ions to nutralize the lysozyme (+8)
and cationic ligands.

Does my setting make sense?
Do you have any suggestion about this ?

Thank you
Lin

----- Original Message -----
From: Thomas Cheatham <tec3_at_utah.edu>
Date: Wednesday, May 27, 2009 5:51 pm
Subject: Re: [AMBER] Why NaCl or KCl solution?
To: AMBER Mailing List <amber_at_ambermd.org>

>
> > In the protein solution, it might be difficult to set PH value
> for it.
>
> Yes, just to clarify, pH=7 means 1 H+ (or H3O+ as RCW suggested)
> per 10
> million waters. As our simulations are typically much smaller than
> this,
> we typically do not include H+... Perhaps at pH=5 (1 per 100,000
> waters)
> maybe we'd add it. Certainly at pH=2 or less. What pH are you
> trying to
> represent?
>
> > In stead, people embed protein into NaCl or KCl solution.
>
> Look at experimental conditions... Most involve some salt (it is
> pretty
> hard to pull out all the salt except with severe dialysis; some
> biomolecules will denature at low salt); physiological salt is
> ~200mM.
>
> Also, if the system is net-charged this make no physical sense; the
> charge
> needs to be neutralized. [Technically you can still run with a net-
> charge
> in Ewald (search the archives), but physically it makes no sense].
>
> The choice of salt depends on what experimental conditions you are
> trying
> to reproduce.
>
> --tec3
>
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