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 - 10:48:30 CDT

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_at_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_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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