getS2
getS2 is a TCL script for get S2 values (Order parameter) from your simulations.
Order parameter is a measure of flexibility from range 1-0 where 1 is absolutly rigid and 0 flexible. If your experimental values are close to simulated, congratulations!, your simulations are closer to represents behavior of your experiments.
Requisites
- VMD >= 1.9.2
Usage
first charge the function (and your simulation) on VMD TK console:
source getS2.tcl
then:
orderparam-protein "protein"
and go for a coffee, the output is a file called "s2.dat" with the resid number and corresponden order parameter value.
Times
getS2 can't be parallelized so the times increases as long as simulated time you have (frames), 5000 frames can take 1 hour in and standar pc.
CITATIONS
the formula was extracted from:
- Indira Chandrasekhar, G. Marius Clore, Attila Szabo, Angela M. Gronenborn and Bernard R. Brooks. A 500 ps Molecular Dynamics Simulation Study of Interleukin-lfl in Water Correlation with Nuclear Magnetic Resonance Spectroscopy and Crystallography. J. Mol. Biol. (1992) 226, 239-250.