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, > [EMAIL PROTECTED] University of Cambridge, > [EMAIL PROTECTED] 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@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 [EMAIL PROTECTED] > 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 ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
