AMBER Archive (2009)

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

From: Jayalakshmi Sridhar (jsridhar_at_xula.edu)
Date: Tue Jun 09 2009 - 10:44:39 CDT

In VMD for the .prmtop top, the file format is AMBER7 parm and for the .mdcrd files it is AMBER Coordinates with the molecule *.prmtop selected for the load files for option.

----- Original Message -----
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Date: Tuesday, June 9, 2009 10:36 am
Subject: Re: [AMBER] DNA as well as protein distorted during MD run in sander

> 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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