Thanks Thomas.
In addition, my protein has 10 alpha helices. During the whole production MD, each of helices 1-4 can only move in a rather narrow space, however each of heleices 5-10 can move in a rather large space.
Will you please suggest by which parameter we can use to describe the space (or deviation) a helix can move?
As for helices 5- 10 can move in a rather larger space in comparison with helicex 1-4, does this mear helices 5-10 have much important biological function? What is your opinion?
Cheers,
Acoot
________________________________
From: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
To: Acoot Brett <acootbrett.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, 23 June 2012 8:40 PM
Subject: Re: [AMBER] How to explain this phenomenon is production MD
Hi,
> I select 2 specific atoms at each sides of the protein, initially the
> distance between those 2 specific atoms is between the 2 atoms is about 80
> A. After 2000 ps, the distance between those 2 specific atoms changes to
> about 85 A. After about another 2000 ps, the distance between those 2
> specific atoms change backs to about 80 A.
well, that strongly depends on what atoms you select. I think that
movement between 80-85A would be prefectly normal for distant side chains,
but it is much more informative if you visualize your structure, calculate
rmsd values and radius of gyration informations to understand the
conformational changes going on.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sat Jun 23 2012 - 18:30:03 PDT
