[MMTK] MMTK questions

Matias Saavedra matias_saavedra at yahoo.com
Fri Jul 29 18:56:05 CEST 2005


hi Nathalie, 

I use Amber94, because i need to consider all the
intramolecular interactions detail.

Matias


--- Nathalie Reuter <Nathalie.Reuter at bccs.uib.no>
wrote:

> Hi Matias,
> 
> what force field do you use to perform the normal
> modes calculation?
> 
> Regards,
> Nathalie
> 
> 
> Matias Saavedra wrote:
> 
> >Hi, two simple questions:
> >
> >1) If i minimize a protein system, i perform a
> Normal
> >Modes analysis, and the i make a single mutation in
> >the already minimized system, to perform a new
> Normal
> >Modes analysis... the results of the second
> analysis,
> >in terms of deformations energies or amplitudes,
> are
> >comparable to the results of the first one? I ask
> that
> >because i know that deformation energies and
> >amplitudes of movement are system-dependent
> >(qualitative), and can not be directly compared
> >between diferent systems (proteins)... but what
> about
> >a system that have been slightly modified by a
> single
> >mutation?
> >
> >2) Can i use the minimized protein to make a single
> >mutation and then perform directly a new Normal
> Modes
> >analysis without the need of a new minimization
> step?
> >(i want to perform several Normal modes analysis in
> >proteins modified by single mutations, and i want
> to
> >avoid the time consuming minimization at each
> >analysis).
> >
> >thanks.
> >
> >
> >
> >
> >		
>
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> 
> 
> 


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