Thank you. When I selected "amber coordinates with periodic box" it worked. Thanks for taking time to resolve my problem.
----- Original Message -----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tuesday, June 9, 2009 10:48 am
Subject: Re: [AMBER] DNA as well as protein distorted during MD run in sander
> well like I said in my first reply, if you have a periodic box
> then you need
> to select it in VMD. what's happening is that the box coordinates are
> shifting everything by a multiple of 3, which appears fine for the
> water (3
> atoms) but not for the solute. I bet if you make sure you use "amber
> coordinates with periodic box" then it will be fine.
>
>
> On Tue, Jun 9, 2009 at 11:44 AM, Jayalakshmi Sridhar
> <jsridhar.xula.edu>wrote:
> > 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.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.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.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.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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Received on Wed Jun 10 2009 - 01:09:34 PDT
