From: Jack Bulat (jack.bulat_at_gmail.com)
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!
Best,
Jack Bulat
On Jan 15, 2013, at 6:45 PM, Siri Søndergaard <siris2501_at_gmail.com> 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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