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 ?
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 07 2013 - 09:30:03 PST
