From: Gaurav Sharma (
Date: Wed Jan 31 2007 - 15:06:46 CST

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.


Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970