AMBER Archive (2006)

Subject: Re: AMBER: RMSD: is it related to flexibility?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Oct 04 2006 - 06:40:04 CDT

RMSD isnt' really flexibility, but you can calculate the
fluctuations in position during the dynamics. This is
flexibility. Whether the simulations can show this or not
depends mostly on the timescale of the motion . Do your
experiments tell you this?

a a wrote:

> Dear All,
>
> I got two protein structures with different performance on the loop
> mobilitiy, one of them move very fast, another one is about 10 time
> less flexible, based on our experimental data.
>
> I could like to ask if it is sensible to do molecular dyanmics
> calculations if I could like to get an explaination for these
> differences, how can I determine the flexibility of a structure? Did
> the RMSD analysis could tell the flexiblity of two loop?
>
> Best regards,
>
> Ann
>
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