Re: [AMBER] how to do analysis of the local structure

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 11 Mar 2010 06:31:38 -0500

you don't say what kind of help you need. there are many papers published on
villin headpiece simulations, so I suggest finding one with use of Amber and
looking carefully at the methods section. The tutorial can also help you get
started with Amber- it isn't clear if you have used it before, or are asking
how to use it.
email the list again when you have a specific question about the simulations
or Amber.

this article might be a good place to start:
Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D. and Simmerling, C.,
*Reconciling
the Solution and X-ray Structures of the Villin Headpiece Helical Subdomain:
Molecular Dynamics Simulations and Double Mutant Cycles Reveal a Stabilizing
Cation-Pi Interaction*, Biochemistry, 46:3624-3634 (2007)

2010/3/11 Nancy <song_jianing_hi.126.com>

> Hi,
>
>
> My simulation system is villin headpiece , a small peptide .It includes
> ASP,GLU and other residues.We expect there will be coupling between COO- in
> the side chains of ASP,GLU and amide-I mode(primarily C=O mode) of the
> backbone , so I want to do some annlysis of the local structure to see
> whether there will some changes in the region around ASP,GLU and backbone
> after I perform MD simulation with AMBER FF03 based on the XRD structure of
> villin headpiece.
> Can you give me some help? Thank you very much!
>
> sincerely
> Nancy
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Received on Thu Mar 11 2010 - 04:00:04 PST
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