[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

-- 
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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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