Respected Mr. Jason
Many thanks for your reply.
I have a trinucleotide system and I solvated the system by the following
command
"solvateOct NUC TIP3PBOX 9.0"
The output is as follows:
Volume: 39543.708 A^3 (oct)
Total mass 19667.242 amu, Density 0.826 g/cc
Added 1039 residues.
Before that I have neutralized the system by the following command:
"addions RNA Na+ 0"
The ouput is"
"2 Na+ ions required to neutralize."
These two Na+ ions are required only to neutralize the two -ve charge of
two phosphates. But the ionic strength of the experimental system is
different as I mentioned in my previous mail. As we know the conformation
of RNA systems depends on the ionic strength of the solution, I am thinking
that if it is possible to setup the same experimental ionic strenght for my
system. In this case what should I do ? First I want calculate the number
of MgCl2 and NaCl molecule required for my system and then how to add these
ions in my solvated system.
I also want to know the logic behind. what about the phosphate buffer,
pH=7.0 and EDTA ?
Actually I want to reproduce the experimental(NMR) sugar pucker of the
residues from simulated trajectory. But after a very long simulation
(700ns) the system still not converged and not reproducing the experimental
observation exactly with 2 Na+ ions required for neutralize the system.
Thanks again.
Sincerely
---indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Thu, Feb 7, 2013 at 8:00 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Feb 7, 2013 at 3:23 AM, Indrajit Deb <biky2004indra.gmail.com
> >wrote:
>
> > Dear Amber Users,
> >
> > I have a small nucleic acid system that I want to simulate.
> >
> > 1 mM of this system is in 0.7 ml 25 mM phosphate buffer, pH 7.0,
> containing
> > 25 mM NaCl, 10 mM MgCl2 and 0.2 mM EDTA for NMR study.
> >
> > I want to prepare same experimental setup for my system.
> >
>
> It's highly unlikely you will be able to do this. For example, I recently
> calculated the ionic strength of one of my simulations where I added a 10
> Angstrom solvent buffer around a 130-residue protein, after which I added
> 15 Cl- and 6 Na+ total ions (the protein was +9). The resulting
> concentration was 200 mM. If I had added just 1 Na+ and 1 Cl- ion, the
> concentraton would've still been ~20 mM (and I would not have been able to
> neutralize my system).
>
> In order to simulate such small concentrations of so many compounds, you
> would need an incredibly large volume with a very large number of water
> molecules. And to make matters worse, there are no good parameters for
> magnesium ions.
>
> Before running these simulations, you really should have a well-formed
> question that you want to ask with a hypothesis about what you think will
> happen. This is what you should use to design your experiment -- it is
> unlikely that everything in your solution will be necessary to gain insight
> from computation.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Feb 07 2013 - 09:30:03 PST
