[gmx-users] normal mode analysis

[Bert de Groot]

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
want.

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).

best,

Bert

______________________________________
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
http://www.mpibpc.mpg.de/groups/de_groot