AMBER Archive (2009)

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

From: Jayalakshmi Sridhar (
Date: Tue Jun 09 2009 - 10:33:51 CDT

Hi Carlos,
While loading the MD files on VMD< I first load the polYAT_wat.prmtop file and then load the polyAT_wat_md1.mdcrd and then polyAT_wat_md2.mdcrd files for the polYAT_wat.prmtop file. As given in the tutorial, I can see the water molecules spreading out. I even tried reimaging with ptraj and tried to visualize it. But I still see the bonds of the DNA molecules stretched out. The plot of energy, pressure, temp, volume look similar to the ones in the tutorial. The backbone rms file does not look very dissimilar. I am attaching those files here.

----- Original Message -----
From: Carlos Simmerling <>
Date: Tuesday, June 9, 2009 9:38 am
Subject: Re: [AMBER] DNA as well as protein distorted during MD run in sander

> 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
> withexplicit 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.
> >
> > _______________________________________________
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> >
> >
> >
> >
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