Re: vmd-l: DNA and low pH

From: Peter Freddolino (
Date: Wed Jan 31 2007 - 19:51:26 CST

The backbone is almost certainly going to be partially neutralized by
tightly bound divalent cations, but you'd have to find a reliable value
for the pKa of the DNA backbone to see if it needs protonation state
modifications (I don't know it offhand). If you did need to protonate
some portions of the backbone you'd need to find or make parameters for
the modified backbone (I'm not aware of any that currently exist) just
as you would for any other novel residue.

Gaurav Sharma wrote:
> Hi All,
> I want to study DNA-protein interaction at low pH.
> For protein I can use the protonated forms of His, Glu and Asp but I
> am not sure what changes to make in the dna structure to simulate low
> pH. Is the negative charge on the dna partially neutralized at low pH
> (~4)? If yes, how can I simulate it using NAMD?
> Any help is appreciated.
> Thanks,
> Gaurav

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