bio3d (version 2.1-2)

sdENM: Index for the sdENM ff

Description

A dictonary of spring force constants for the sdENM force field.

Usage

data(sdENM)

format

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.

source

Dehouck Y. & Mikhailov A.S. (2013) PLoS Comput Biol 9:e1003209.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

## 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]

## and distance range [4.5, 5)
sdENM[1:5, 1:5, 2]

## amino acid pair A-P, at distance 4.2
sdENM["A", "P", 1]

## for use in NMA
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
modes <- nma(pdb, ff="sdenm")