Re: [AMBER] How to set salt concentration

From: Nada Afiva <nadaafiva.gmail.com>
Date: Sat, 4 Jul 2020 02:58:26 +0700

Dear Clorice and Amber list,
Yes, you are right. So it should be 61 Na+ and 50 Cl- ions.
One thing, as the formula apply when No/Q >=1.
In my case, No/Q= -5.01. Is the formula still apply?
Thanks so much for your helps.

Best regards,
nadaafiva

Pada tanggal Sab, 4 Jul 2020 pukul 02.10 Clorice Reinhardt <
clorice.reinhardt.yale.edu> menulis:

> Hi Nadafiva,
> I think you need to remember to keep the sign in using the equations in the
> forum post. If you only plugged in Q=11, instead of Q=-11, this would
> explain the numbers you obtain.
> All the best,
> Clorice
>
> On Fri, Jul 3, 2020 at 3:01 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> > Dear Sir,
> > 50 Na+ and 61 Cl- ions were calculated according to this:
> > http://archive.ambermd.org/202002/0194.html
> >
> > After that would neutralize by adding a number of Na+, so final
> > charge would be zero. Please correct me if I am wrong.
> > Thanks.
> >
> > nadafiva
> >
> > Pada tanggal Jum, 3 Jul 2020 pukul 20.45 David A Case <
> > david.case.rutgers.edu> menulis:
> >
> > > On Fri, Jul 03, 2020, Nada Afiva wrote:
> > >
> > > >I have protein+RNA+ligand with charge -11.00.
> > > >I want salt concentration 0.15 M. Using your formula,
> > > >I have to add 50 Na+ and 61 Cl- ions.
> > >
> > > This seems wrong: you want more cations than anions, in order to
> > > neutralize the negative charge of the solute.
> > >
> > > ....dac
> > >
> > >
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Received on Fri Jul 03 2020 - 13:00:03 PDT
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