[gmx-users] CRY-ED question

[Daan van Aalten]

Hi Ruben

No you can't. However what we have done in the past is to

1) fit your two crystal structures on your reference frame (of course
   making sure they have the same atoms etc)
2) calculate a vector describing the structural transition in hyperspace
   simply by subtracting the coordinates between the two structures
3) normalize (!!!) this vector
4) now you can project your ED eigenvectors onto this vector to see if
   the experimentally observed conformation change is at all covered by
   your MD simulation!

Daan

On Tue, 27 Jul 2004, Ruben Martinez Buey wrote:

> > Hi all,
>
> I would like to compare my MD/ED simulations with a CRY-ED analysis of my protein,
> but I only have two crystal structures. Can I correctly deduce the essential
> dynamics from only two experimental conformations?
>
> Thanks a lot in advance,
>
> Bests,
>
> Ruben
>
>
> --
> ___________________________________________
>
> Rubén Martínez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biológicas (CIB-CSIC)
> C/ Velázquez, 144,  28006  MADRID (SPAIN)
> Tlf: +34-91-561 18 00 ext. 4380
> Fax: +34-91-562 75 18
>
>
>


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Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
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