AMBER Archive (2008)

Subject: Re: AMBER: Calculate number of ions

From: Ruchi Sachdeva (ruchi.imt_at_gmail.com)
Date: Wed May 14 2008 - 02:24:08 CDT

Hi Dong,

Autoionize plugin does not substract the volume occupied by the protein. It
calculates the volume occupied by water as: volume per water molecule * no.
of water molecules present in the system.

I don't know how AMBER calculates the no. of ions but you can go to this
link <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3943.html> and
see how VMD autoionize plugin does this. Hope this would help you!

Ruchi

On 5/13/08, Mathy Froeyen <matheus.froeyen_at_rega.kuleuven.be> wrote:
>
>
> 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
>
>
> mathy
>
> _____________________________________________
>
> 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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