AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 09 2009 - 10:36:50 CDT

if the data is the same, then I think it's the vmd imaging. what file format
in vmd are you selecting?

On Tue, Jun 9, 2009 at 11:33 AM, Jayalakshmi Sridhar <jsridhar_at_xula.edu>wrote:

> 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 <carlos.simmerling_at_gmail.com>
> 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
> > <jsridhar_at_xula.edu>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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