feenstra at chem.vu.nl
Thu Apr 10 09:00:04 CEST 2003
Ruben Martinez Buey wrote:
> Hi all,
> Thanks alot for your reply,
> I only want to see global motions of the bacbone or C-alpha , starting from a
> 2.7 A. resolution structure, so maybe it is impossible to minimize until Fmax < 0.0001?
> and maybe it can work with shorter minimizations?
Why not run a short MD and do Essential Dynamics analysis?
Use g_covar for the covariance analysis, and g_anaeig for
display/projection of the results. IMHO, for a protein, this
gives more realistic results for the dynamics of the system
than a normal modes analysis.
If you're worried about getting out of a local minimum,
you could always run the MD at low temperatures, say 100K.
(Don't know if that has been done previously by someone.)
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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