Dear John,
Input to ptraj or cpptraj:
trajin ../data/pp1.eq6.mdcrd.gz
distance Ends :1.N :245.C out EndDistance.dat
This makes a file "EndDisatnce.dat" with what you want. Cpptraj is better because it can put several distance measurements in one file and label the header. Here my header is "Ends".
John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212
-----Original Message-----
From: Beale, John [mailto:John.Beale.stlcop.edu]
Sent: Friday, March 02, 2012 7:58 AM
To: amber.ambermd.org
Subject: [AMBER] Distance plot
I hope that someone can help me. I need to plot the end-to-end distances vs. MD time for some short protein chains. I assume that the "distance" action command in either ptraj or cpptraj would form the basis of what I want to do. How can I compute the distances at my trajectory time points so that I can plot the data?
Thanks!
John
John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy Department of Neurology, Washington University School of Medicine
Office: 314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460
John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
bealej.neuro.wustl.edu<mailto:bealej.neuro.wustl.edu>
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Received on Fri Mar 02 2012 - 07:00:01 PST
