[gmx-users] PCA of crystal structures

Ullmann, Thomas thomas.ullmann at mpibpc.mpg.de
Mon Dec 22 09:04:35 CET 2014


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,
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

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
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