As one (of many published) approaches to this problem using AMBER see --
Pfeiffer S, Fushman D, Cowburn D
Simulated and NMR-derived backbone dynamics of a protein with significant
flexibility: A comparison of spectral densities for the beta ARK PH domain
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 123 (13): 3021-3036 APR 4 2001
And
Pfeiffer S, Fushman D, Cowburn D
Impact of Cl- and Na+ ions on simulated structure and dynamics of beta ARK1
PH domain
PROTEINS-STRUCTURE FUNCTION AND GENETICS 35 (2): 206-217 MAY 1 1999
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Varsha Goyal
Sent: Friday, December 16, 2005 7:03 PM
To: amber.scripps.edu
Subject: AMBER: About Salt concentration
Dear Amber users,
I was wondering what happens of we use extra sodium
and chloride ions during Molecular Dynamics ( meaning
use some particular salt concentration)?
Is it necessary? What difference does it make?
Happy Holidays!!!!!!
Thanks a lot in Advance,
Varsha Gupta
---
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Received on Wed Dec 21 2005 - 21:53:01 PST
