AMBER Archive (2008)

Subject: AMBER: Gohlke in-house iRED Simulated Order Parameter Script

From: Titus, Jamie (bairdje) (BAIRDJE_at_ucmail.uc.edu)
Date: Thu Aug 21 2008 - 07:53:09 CDT

Hello all,

I am attempting to calculate order parameters using the iRED approach. In reading the supplemental materials with the paper, 'Starting structure dependence of NMR order parameters derived from MD simulations' (http://www.biophysj.org/cgi/data/biophysj.108.132811/DC1/1), it was stated that "The S2 values were then calculated with an in-house script." Does anyone know if this script is available somewhere, or does anyone have a script available that they would like to share?

Also, clarification of the discussion in thread http://structbio.vanderbilt.edu/archives/amber-archive/2008/2351.php would be helpful considering that the previously mentioned Gohlke paper uses the iRED approach and the Hornak approach to calculate S2, while the thread ends with the AMBER user only using the Hornak approach because the iRED approach failed to work for him.

Thanks for any help!

Jamie

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