On Feb 7, 2013 9:25 AM, "Indrajit Deb" <biky2004indra.gmail.com> wrote:
>
> I made a mistake. The command -"addions RNA Na+ 0" will be "addions NUC
Na+
> 0"
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
>
>
> On Thu, Feb 7, 2013 at 10:48 PM, Indrajit Deb <biky2004indra.gmail.com
>wrote:
>
> > 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 ?
Perhaps you should consider what these mean. Very small concentration of
H+? Protonation states of certain residues?
> >
> > Actually I want to reproduce the experimental(NMR) sugar pucker of the
Sugar pucker? Isn't this more dependent on related dihedral and angle
paprameters?
> > 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.
Since you have the computational resource, why not using a larger box?
Based on the volumn, it is not difficult to calculate the number of ions
required for a certain concentration.
> >
> > 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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Received on Thu Feb 07 2013 - 11:00:03 PST
