[gmx-users] normal mode analysis

Bert de Groot bgroot at gwdg.de
Fri Dec 21 13:26:01 CET 2007

Robert Fenwick wrote:
> Hi,
> I am interested in comparing the normal modes of a protein with and
> without a ligand. I have already computed the lowest 100 normal modes
> for the protein (eigenvec_a.trr) and the protein:ligand complex and have
> reduced the protein:ligand eigenvec_b.trr to the protein by issuing;
>> trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
>> select 0 [System]
> Where:
> + nm_a.tpr is the tpr file of the protein alone
> + eigenvec_b.trr is the trajectory of the protein:ligand
> + eigenvec_c.trr is the new trajectory of the complex minus the ligand
> coordinates
> What I want to do now is compare the eigenvec_a.trr and eigenvec_c.trr
> files to see the mode overlap between the free and bound protein.
> What I can not understand how to remove the effects of rotation and
> translation of the protein with respect to the ligand that will be
> present in the eigenvec_c.trr. Is it possible to do this type of
> analysis in GROMACS and how can I go about it?

if you remove part of the system e.g. the ligand) from a set of eigenvectors
you'll end up with non-orthogonal vectors. This is almost certainly not what you

I'd suggest for each set of normal modes (with and without ligand) to generate a
corresponding ensemble at a certain temperature with g_nmens. Then from those
trajectories you can cut out the ligand to generate two protein-only
trajectories, on which you then can run a PCA with g_covar (either separately
and calculate eigenvector overlaps, or concatenate both trajectories and look at
projection differences).



Bert de Groot, PhD

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

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

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