Re: DNA terminals and charges

From: Jack Bulat (
Date: Tue Jan 15 2013 - 22:13:24 CST

Hi Siri,

The pKa2 of phosphoric acid is 7.2, and in general is within the 6.8-7.2 regime for phosphate-containing molecules. That means that, at pH 7, you'd expect a 1:1 ratio of -1 and -2 charges. I have previously modeled with just -1 for solvent ionization purposes at physiological pH. In some of the literature I've seen, they just stick with -1.

How long is the DNA segment? Also, are you simulating a population of molecules or just one? Maybe you can specify this and then that would help others better advise you.

Hope this helps you a bit!

Jack Bulat

On Jan 15, 2013, at 6:45 PM, Siri Søndergaard <> wrote:

> Hi
> I'm about to run simulations on DNA and was wondering what the terminals should be like? The CHARMM topology does not have a patch for charged phosphate terminals but when the pH is ~7 shouldn't the terminal phosphates have a charge of -2?
> Thanks
> Siri Soendergaard

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