AMBER Archive (2003)

Subject: Re: problem on MD simulation of damage DNA

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu May 01 2003 - 15:20:02 CDT

you might look at our article on conformational
sampling of DNA with a bulky pyrene subsitution,
see JACS 2002, 124, 12154-12164

others may have suggestions as well.
carlos

----- Original Message -----
From: "Shuang Ding" <sd517_at_nyu.edu>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, May 01, 2003 4:11 PM
Subject: problem on MD simulation of damage DNA

> 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
>
>