AMBER Archive (2009)

Subject: RE: [AMBER] rmsd_dna

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Jul 08 2009 - 20:55:53 CDT

Dear Dr. Carlos Smmreling ,

I have built some model and i have minimized and equillibriated it
and having the .rst files ,

is it possible to find the rmsd for the whole trajectory ,
with the model (.rst) files
---------------------------------------
I saw the input for ptraj as
trajin < >
trajout <>
rms first mass out * .rms time 0.1
-----------------

in the input file how one should give the .rst

of the individual dna , and compare it with the trajectory .

thanking you

regards
balaji

> From: carlos.simmerling_at_gmail.com
> Date: Wed, 8 Jul 2009 14:21:29 -0400
> Subject: Re: [AMBER] rmsd_dna
> To: amber_at_ambermd.org
>
> have you looked at the DNA MD tutorial on the Amber web site? I think it
> covers this very well. let us know if you have specific problems with steps
> in the tutorial.
>
> On Wed, Jul 8, 2009 at 12:15 PM, balaji nagarajan
> <balaji_sethu_at_hotmail.com>wrote:
>
> >
> > Dear amber ,
> >
> > I have done dynamics of a DNA ,
> >
> > and I have built some model for the same ,
> >
> > I would like to check the Rmsd of my each model with the whole trajectory ,
> >
> > any one can tell me how to give the input script for ptraj ,
> > if one considers all the atoms
> >
> > thanking you
> > regards
> > balaji
> > UOM
> >
> >
> >
> >
> >
> >
> > _________________________________________________________________
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