AMBER Archive (2003)

Subject: charge neutralization in DNA

From: Mahadevan Seetharaman (maha_at_vwl.medc.umn.edu)
Date: Tue Feb 18 2003 - 13:08:55 CST

Hi,

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.

Thanx in advance for your responses,
Mahadevan