AMBER Archive (2008)

Subject: Re: AMBER: Calculate number of ions

From: Mathy Froeyen (
Date: Tue May 13 2008 - 02:50:29 CDT

Hi Dong,
I don't think the volume of the solute is used
when going from Molar to number of ions in the box.

You have to consider the central
protein/DNA immersed in an infinit box
(implemented as periodic images).
So in fact you have an infinit dilution
for the protein, but not for the ions.

I tried out the MeadIonize to add ionic strength
around a (already neutralized by Na+) RNA strand. The box was 36x36x60
and I requested a IS of 0.5 mol/liter.
MeadIonize gave back 23 Na+ and 23 Cl- ions to add:

(0.5 Mol) * (6.02*10^23) / 1dm^3 / ((10^9)^3 * (Ang^3/dm^3))
-> 3*E-4 molecules/Ang^3
-> box = 77760 Ang^3 -> 23.328 molecules



On Sat, 10 May 2008, Dong Xu wrote:

> Hi All,
> I have a question regarding the correct procedure of calculating exact
> number of ions needed to reach a certain salt concentration. Say I
> want to have 0.15M NaCl in my system and it's already neutralized and
> solvated with "solvatebox protein TIP3PBOX 10.0" in tleap. I measure
> the water box dimensions in VMD and I calculate the number of ions
> based on the volume of the water box. But the problem is that the
> number of ions calculated this way is always much larger than the
> number of ions calculated from VMD autoionize plug-in. I'm guessing
> autoionize plug-in subtracts the volume occupied by the protein? It's
> a hassle to use the VMD plug-in because a CHARMM style psf file for
> the solvated system is required. So, I was wondering what is the
> correct AMBER way of calculating number of ions?
> Thanks a lot!
> Dong Xu
> -----------------------------------------------------------------------


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