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

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Wed May 18 10:14:20 CEST 2005

> 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
this problem was discussed by Karplus et al. in the paper J. Comp. Chem.
16, 1522-1542 (1995)


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