[gmx-users] normal mode analysis

Robert Fenwick rbf22 at mole.bio.cam.ac.uk
Fri Dec 21 12:48:14 CET 2007


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  

 > trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr
 > select 0 [System]

+ 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?



         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.

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