AMBER Archive (2008)

Subject: Re: AMBER: NMR average structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Aug 20 2008 - 12:50:28 CDT

there are many things that can cause disagreement. individual
structures have thermal fluctuations, simulation conditions (pH etc)
may not match the experiment, simulations may have inaccurate
parameters, and the "experimental" structures are based on modeling
using the NMR restraints. if the system is not well determined by the
restraints, then the actual NMR "structure" may not reflect
experimental reality. Often it is a good idea to compare simulations
to the primary experimental data (NOEs etc) rather than a structure
model that was generated using a simple force field and the NMR data.
also it is not usually good to compare the "final" structure from a
simulation but rather compare the average structure, or even better
compare a representative structure from a method such as cluster
analysis.

On Wed, Aug 20, 2008 at 1:42 PM, Gigil Toton <toton.mahor_at_yahoo.com> wrote:
> Hi all,
>
> if we suppose that the NMR input structure, which is defined in the
> biological conditions is the average conformation, is it logical to get some
> differences in the final structure of MD simulations which is performed in
> the same biologic conditions. as i have see in papers the authors compare
> the initial structure and the final one which they get from md simulations
> without doing any changes ( like mutations). could it be a true statement.
>
> thanks
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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