Dear Amber community members,
I wish to perform principal component analysis (PCA) on MD trajectories to
understand what determines the major movements in the receptor and among
different trajectories which movements in helices/beta-sheets/loops are
different/similar.
If I understand correctly this can be done using the "matrix", "projection"
and 'analyze" commands in cpptraj.
http://archive.ambermd.org/201209/0128.html,
http://structbio.vanderbilt.edu/archives/amber-archive/2009/3812.php,
http://structbio.vanderbilt.edu/archives/amber-archive/2009/3809.php,
http://structbio.vanderbilt.edu/archives/amber-archive/2009/3800.php,
http://archive.ambermd.org/201209/0117.html
But as there are no detailed explanation offered to the meaning and usage
of these commands/flags in the manual, I am not able to understand how to
use them with respect to my situation. (AmberTools manual pg. 191, 198 and
199). Also thread (mentioned above) although were useful, did not really
clear how can I use them for my purpose.
Did I miss something in the manual? please suggest.
My system is a protein with :1-271 protein and 272 ligand. I wish to
understand movements with H-3, H-4, H-11 and H-12 and loop 5 and beta-sheet
regions.
I have 200 ns MD simulation trajectories to be analyzed.
In JACS, 2011, 133, 13197 (10.1021/ja205313h), the authors report similar
study using GROMACS. I hope this is analysis can be done in Amber too, can
we?
Thanks in advance.
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Feb 18 2013 - 00:00:03 PST
