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

Marc Baaden baaden at smplinux.de
Tue May 17 17:05:22 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

 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

More information about the gromacs.org_gmx-users mailing list