Re: [gmx-users] surrounding a peptide by ions of magnesium

[Justin Lemkul]

On 5/2/13 7:33 AM, Mohan maruthi sena wrote:

Hi ,
 Thanks for a quick reply. Sorry for not being clear,  I want to
surround the peptide with just ions(sodium). How can I  do this?



genbox -ci -nmol

You will need a coordinate file for a single Mg2+ ion to be inserted, which is 
trivial to create by hand.  I don't know how the ion force field parameters will 
behave in the absence of explicit solvent.  Are you planning to use implicit 
solvent?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] surrounding a peptide by ions of magnesium

[Mohan maruthi sena]

Hi ,
Thanks for a quick reply. Sorry for not being clear,  I want to
surround the peptide with just ions(sodium). How can I  do this?

Thanks,
Mohan


On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul  wrote:

>
>
> On 5/2/13 12:38 AM, Mohan maruthi sena wrote:
>
>> Hi all,
>> I have system consisting of a peptide(alpha-helix), I want the
>> peptide to be surrounded by magnesium ions(instead of water). How can i do
>> this gromacs? How can I find the concentration of magnesium ions. just
>> like
>> in solution we have 0.5 Molar  Mg+2  solution, My question how can  find
>> concentration by increasing number of ions.
>>
>>
> I don't fully understand what you're trying to do, especially in the
> absence of solvent, but I'll venture some simple advice.  Concentration is
> just the number of moles per unit volume.  Simple unit conversion exercises
> will tell you how many ions are needed to achieve whatever target
> concentration you're looking for.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] surrounding a peptide by ions of magnesium

[Justin Lemkul]

On 5/2/13 12:38 AM, Mohan maruthi sena wrote:

Hi all,
I have system consisting of a peptide(alpha-helix), I want the
peptide to be surrounded by magnesium ions(instead of water). How can i do
this gromacs? How can I find the concentration of magnesium ions. just like
in solution we have 0.5 Molar  Mg+2  solution, My question how can  find
concentration by increasing number of ions.



I don't fully understand what you're trying to do, especially in the absence of 
solvent, but I'll venture some simple advice.  Concentration is just the number 
of moles per unit volume.  Simple unit conversion exercises will tell you how 
many ions are needed to achieve whatever target concentration you're looking for.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] surrounding a peptide by ions of magnesium

[Mohan maruthi sena]

Hi all,
   I have system consisting of a peptide(alpha-helix), I want the
peptide to be surrounded by magnesium ions(instead of water). How can i do
this gromacs? How can I find the concentration of magnesium ions. just like
in solution we have 0.5 Molar  Mg+2  solution, My question how can  find
concentration by increasing number of ions.

Thanks for a reply in advance,

Mohan
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