AMBER Archive (2003)

Subject: problem on MD simulation of damage DNA

From: Shuang Ding (sd517_at_nyu.edu)
Date: Thu May 01 2003 - 15:11:04 CDT

Hi,

I am trying to run MD simulation of a damage 11mer DNA that has a bulky adduct to one base. The modified base move out double helix, and drive two strands separate at simulation process. I have tried to change some parameters, but it didn't work. How to fix it?
Thanks a lot.

shuang ding