AMBER Archive (2005)

Subject: Re: AMBER: Analysing my simulation data..

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Jun 18 2005 - 11:47:06 CDT

The new tutorial number 4 has RMSD calculation and H-Bond analysis.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.htm

I think this tutorial is very useful on understanding how to treat a
structure and anaylze it. It uses VMD to find the RMSD values, and MMTSB
tool to do H-Bond analysis. Good luck.

On Sat, 18 Jun 2005, Varsha Goyal wrote:

> Dear Vijay,
> I guess using VMD would be best idea to calculate RMSD
> value. There is tutorial online on AMBER website for
> how to use VMD and its well ec\xplained there how to
> calculate RMSD.
>
> Vijay Manickam Achari <vjrajamany_at_yahoo.com> wrote:
>
> > Dear Amber users,
> >
> > I am a novel user of Amber and I have done my
> > simulation on micelle strucure in explicit water.
> >
> > Here I would like to get some advice and guidance
> > from
> > all the professionals out there the procedure that I
> > must follow to get a reliable results of my
> > analysis.
> >
> > I would like to calculate properties like
> > RMSD value,
> > Radius of Gyration, and
> > H-bond for my micelle structure.
> >
> > In order to calulate the above properties do I need
> > to
> > reimage the micelle structure?
> >
> > Is there any other pre-adjustments or pre-setup I
> > need
> > to do with the output files such as xxxx.mdcrd,
> > xxxx.out, xxxx.rst before starting calculation?
> >
> > I really appreciate your kind advice and guidance.
> >
> > Thank you
> > Vijay.
> >
> >
> >
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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