[MMTK] MMTK questions

Nathalie Reuter Nathalie.Reuter at bccs.uib.no
Fri Jul 29 18:24:47 CEST 2005

Hi Matias,

what force field do you use to perform the normal modes calculation?


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
>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
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