AMBER Archive (2003)

Subject: Re: charge neutralization in DNA

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 18 2003 - 16:27:20 CST

On Tue, Feb 18, 2003, Mahadevan Seetharaman wrote:
>
>
> I have two positively charged N-groups in my DNA 10-mer (duplex). When I
> do "addions unit Na+ 0", only 16 sodium ions are added (understandable,
> since the net charge is -16, 18 phosphates and two N+). I think the system
> should have 18 Na+ ions and 2 Cl- ions instead of 16 Na+ ions. If I want
> to add 18 Na+ ions and 2 Cl- ions to this system, how would I do it, apart
> from doing it manually.
>

You should be able to do the following:

addIons x Na+ 18
addIons x Cl- 2

I don't know if you think this is doing it "manually" or not, but I don't
think there is any simpler approach.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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