Re: [AMBER] Is it possible to plot RMSd VS residue number for a protein?

From: M. Reza Ganjalikhany <ganjalikhany.gmail.com>
Date: Tue, 1 Jun 2010 17:27:20 +0100

Hi Homa,

I'm not sure that they are the same value.
There are papers in which RMSF and also RMSD of each residue have been
reported separately!!

please take a look at following papers:

1- Mol. Biol. (2003) 327, 745757: Protein Dynamics in a Family of
Laboratory Evolved Thermophilic Enzymes.

2- Biophysical Chemistry 78 (1999) 247-257: Long-term molecular dynamics
simulation of copper azurin: structure, dynamics and functionality

3- Phys. Biol. *2 *(2005) S137S147: Protein flexibility using constraints
from molecular dynamics simulations.
Many thanks,
M. Reza


On Tue, Jun 1, 2010 at 12:58 AM, Homa Azizian <homa.azizian.anu.edu.au>wrote:

> Hi Reza,
>
> RMSF is the way that you can measure the fluctuation of each residue.
>
> Best regards
>
> Homa
>
> > Hello all,
> >
> > I ran a 10ns MD simulation with a protein containing 181
> > aa and I want to
> > obtain average value of RMSd for each
> > residue (or alpha carbons) during the last 5ns and then
> > plot it against the
> > residue number.
> >
> > How is it possible to plot RMSd of a protein versus residue
> > number with
> > ptraj? what else could be done to obtain such plot?
> >
> > Ragards,
> > M. Reza
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Received on Tue Jun 01 2010 - 10:00:14 PDT
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