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.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.
> >
> >
> >
> >
> ___________________________________________________________
> >
> > How much free photo storage do you get? Store your
> > holiday
> > snaps for FREE with Yahoo! Photos
> > http://uk.photos.yahoo.com
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> > majordomo.scripps.edu
> >
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://www.rosswalker.co.uk/adsense_alternatives/
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Jun 18 2005 - 17:53:00 PDT
