data(sdENM)
A dictonary of spring force constants for the sdENM force field.
An array of 27 matrices containg the spring force constants for the ‘sdENM’ force field (see Dehouch et al for more information). Each matrix in the array holds the force constants for all amino acid pairs for a specific distance range.
See examples for more details.
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Dehouck Y. et al. (2013) PLoS Comput Biol 9:e1003209.
## Load force constant data data(sdENM) ## force constants for amino acids A, C, D, E, and F ## in distance range [4, 4.5) sdENM[1:5, 1:5, 1]A C D E F A 2.469 3.711 0.988 2.603 4.171 C NA 10.227 3.320 2.923 4.599 D NA NA 3.535 2.786 3.012 E NA NA NA 5.286 4.165 F NA NA NA NA 4.874## and distance range [4.5, 5) sdENM[1:5, 1:5, 2]A C D E F A 3.282 2.792 3.875 3.220 3.105 C NA 1.944 3.478 2.543 4.895 D NA NA 2.025 1.991 4.525 E NA NA NA 4.250 3.288 F NA NA NA NA 3.846## amino acid pair A-P, at distance 4.2 sdENM["A", "P", 1][1] 7.593## for use in NMA pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) modes <- nma(pdb, ff="sdenm")Building Hessian... Done in 0.475 seconds. Diagonalizing Hessian... Done in 0.133 seconds.