AMBER Archive (2008)

Subject: Re: AMBER: Structure comparison-NMR and X-ray structure using AMBER9

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jan 07 2008 - 10:16:16 CST

you might look at an example of this analysis that we did for a single
protein using MD

**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)

also Levy's group (and others) has done more extensive analysis of
differences between
xray and nmr structures, though I am not sure of large-scale studies using
MD.

On Jan 7, 2008 11:11 AM, Prem Prakash Pathak <prempolymer_at_gmail.com> wrote:

> Dear All,
>
> Is there a way to compare NMR ensemble of structures and the X-ray crystal
> structure of a given protein, using AMBER9.
>
> I have a solution structure and the crystal structure of the protein
> exits, so i wanted to make some comparison, and find out and justify the
> differences between them.
>
> Please suggest a way out, in detail.
>
> Happy New year -2008 to All
>
> Regards
> Prem Prakash
>

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