Try selecting AMBER Coordinates with Periodic Box when you load the mdcrd files.
Jesse Ziebarth
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Jayalakshmi Sridhar [jsridhar.xula.edu]
Sent: Tuesday, June 09, 2009 10:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] DNA as well as protein distorted during MD run in sander
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 - 01:09:28 PDT
