AMBER Archive (2009)

Subject: Re: [AMBER] DNA as well as protein distorted during MD run in sander

From: Carlos Simmerling (
Date: Tue Jun 09 2009 - 09:38:14 CDT

the first thing is to determine if it is a problem in the MD run or just in
visualizing the results. often people use the wrong file format in VMD when
loading the trajectory file. can you give us details of what you are doing?
also, if the energies are ok in the MD output, then it's unlikely that the
structure is really distorted and likely the visualization is the problem.
if you are using VMD, make sure to pick "amber coordinates" for DNA with
implicit solvent and "amber coordinates with periodic box" for use with
explicit solvent.

On Tue, Jun 9, 2009 at 10:30 AM, Jayalakshmi Sridhar <>wrote:

> Hi,
> I am new to Amber. I have installed amber10 on a redhat linux machine. I am
> having problems with MD with sander. I am running the first tutorial of the
> DNA in MD as per the instructions. Minimization runs well. But when I try
> the MD, the DNA gets completely distorted. All the bonds in the DNA are
> stretched out. I am using the *.in files given in the tutorial. I am having
> the same trouble with my proteins too. Could there be nay problem with
> sander installation? Where do I look for trouble shooting. Help is greatly
> appreciated.
> Jayalakshmi.
> _______________________________________________
> AMBER mailing list
AMBER mailing list