[gmx-users] PCA of crystal structures

[Ullmann, Thomas]

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
thomas.ullmann at mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--------------------------------------------------------------------------------------------------------------------------

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of neeru sharma [neeru.bioinfo at gmail.com]
Sent: Monday, December 22, 2014 6:04 AM
To: gmx-users at gromacs.org
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 gmx-users-request at gromacs.org.