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 _______________________________________________ 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
