Hi, you can directly project the crystal structures onto the eigenvectors from the PCA with gmx anaeig. It may be necessary to create an index file for each PDB file with an index group that identifies the atoms that correspond to the vector components. Make sure that the order of atoms is the same in the PDB as in the trajectories/structures used in the PCA. For multimeric proteins, make sure that the order of subunits is also the same.
Happy computing, Thomas. -------------------------------------------------------------------------------------------------------------------------- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen, Germany [email protected] www.bisb.uni-bayreuth.de/People/ullmannt -------------------------------------------------------------------------------------------------------------------------- ________________________________________ From: [email protected] [[email protected]] on behalf of neeru sharma [[email protected]] Sent: Monday, December 22, 2014 6:04 AM To: [email protected] Subject: [gmx-users] PCA of crystal structures Dear Gromacs-users, I have carried out MD simulations of a Protein complex starting with the active state conformation a particular crystal structure and have carried out PCA analysis for the same too. Now, I want to identify the location of all the crystal structures of the same protein (Intermediate, active, inactive, mutants etc) on the PCA plots too but I haven't run simulations for all of these. Can anyone suggest me the way to do so? --Neeru Shara C-DAC, Pune, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
