[gmx-users] normal mode analysis

[Florian Haberl]

Hi, 

On Friday, 21. December 2007 12:48, 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?

Fit it first on the same reference structure, i think CA or Backbone atoms are 
enough for this kind of analysis.

g_covar -h (calculating the covariance matrix)
and
g_anaeig -h -inpr (compare the different systems)
should help you 
you can only compare matrix/ trajectories with the same atom number.


>
> Regards,
>
>
> Bryn
>
>
>          ==========================================================
>          R. Bryn Fenwick                Department of Biochemistry,
>          rbf22 at cam.ac.uk                University of Cambridge,
>          bryn.fenwick at cantab.net        80 Tennis Court Road,
>          Tel: +44 1223 766018           Old Addenbrookes Site,
>          Fax: +44 1223 766002           Cambridge, CB2 1GA, UK.
>          ==========================================================
>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------