[gmx-users] CRY-ED question

[Bert de Groot]

Daan van Aalten wrote:
> 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


in fact, you could use g_covar to do these three steps, provided you start
from a nmr-style pdb file (or xtc or any other trajectory format gromacs
supports) containing your two x-ray structures. This would have the advantage that
it's directly compatible to MD output and can be directly analysed by e.g.
g_anaeig.

It's important, as Daan said, to make sure that you have the same atoms and
same ordering for both structures. You'll notice when you use g_anaeig afterwards if
something went wrong though.


> 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
> 



Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________