[gmx-users] RMSF calculations

[Tsjerk Wassenaar]

Hi Gurunath,

Each structure in the NMR ensemble is a fit to the experimental data.
Unlike an MD trajectory, you can not assume that the set of structures
is a proper sample from the Boltzmann distribution, and therefore, the
RMSF can not be expected to correspond to the RMSF of the system. Now,
on a more qualitative level, it is likely that the parts that are less
defined in the NMR ensemble will also have larger RMSFs than the rest,
and could do for a rough comparison.

Hope it helps,

Tsjerk

On Mon, Oct 10, 2011 at 12:22 PM, Gurunath Katagi <gurukatagi at gmail.com> wrote:
> Dear all,
> I have a set of proteins(in pdb format) in which some are solved by X-ray
> diffraction and some by NMR.
> I have done the md simulation of these proteins using gromacs for 30ns [For
> NMR structures, i have taken the first model as the starting structure]
>
> Now, that i want to calculate the RMSF value from the simulations and
> compare with the RMSF values from experimental structures [X-ray/NMR]
> For the proteins with crystal structures , calculation is done using using
> g_rmsf function and the comparison is done.
>
> and  for protein from NMR structure , the RMSF values are calculated from
> the simulation trajectory. But in order to compare these, how does one get
> the RMSF values ? ,since
>  the pdb file doesn't have the b-factors ..
>
> Is it a good idea to use the  NMR ensembles ( usually 20 models from NMR) to
> derive the RMSF  and compare these with simulation results ..?
> or is there any other parameter that i can calculate from NMR models, which
> is similar to RMSF ..?
>
> Thanksin advance ..
>
> Thanking You
> Gurunath
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands