[gmx-users] Normal Mode Analysis on Calphas only ??

Xavier Periole x.periole at rug.nl
Tue May 17 17:45:31 CEST 2005

Marc Baaden wrote:

>we started to do some normal mode calculations on a protein complex
>and several mutants. To simplify things (and because the different
>complexes have different numbers of atoms which makes comparison more
>difficult) we wanted to compare eg Calphas only or per residue only.
>This seems to be more difficult than expected, and I wonder at which
>point this could be done. Current guesses are:
> - "edit"/modify the hessian matrix .mtx file to only include data
>   on Calpha only .. and from then on "standard" procedures
> - "average"/sum up the eigenvectors.trr for each residue (not sure
>   this is correct)
>the last resort kind of solution seems to me
> - extract an ensemble from the NM calculation, do PCA on the Calphas
>   of the ensemble .. but this really seems like serious overkill
>I hope I have just missed the simple, obvious and straightforward solution,
>and that some kind person will point it out to me.
>Thanks in advance,
>  Marc Baaden
>NB: as we want to look at overlaps and this kind of thing it will be
>    important to generate a Calpha based set of EV that is still orthogonal
Hi Marc,

We did something similar with Marco Ceruso on the protein transducin. We 
ran PCA
on a WT and mutants of the Calpha trajectories and made comparisons. We 
just filtered
the trajectories and generated trajectories unclucing only Calpha atoms.
It worked pretty good and the results were very clear. you can check the 
paper (Ceruso,
Periole,Weinstein, in JMB last year)


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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