bio3d (version 2.3-4)

read.crd.amber: Read AMBER Coordinate files

Description

Read coordinate data from an AMBER coordinate / restart file.

Usage

# S3 method for amber
read.crd(file, ...)

Arguments

file

name of crd file to read.

…

arguments passed to and from functions.

Value

A list object of type ‘amber’ and ‘crd’ with the following components:

xyz

a numeric matrix of class ‘xyz’ containing the Cartesian coordinates.

velocities

a numeric vector containg the atom velocities.

time

numeric, length of the simulation (applies to Amber restart coordinate files).

natoms

total number of atoms in the coordinate file.

box

dimensions of the box.

Details

Read a AMBER Coordinate format file.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. http://ambermd.org/formats.html

See Also

read.prmtop, read.ncdf, as.pdb, atom.select, read.pdb, read.crd.charmm

Examples

# NOT RUN {
## Read Amber PRMTOP and CRD files
prm <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))
crd <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))

## Convert to PDB format
pdb <- as.pdb(prm, crd)

## Atom selection
ca.inds <- atom.select(prm, "calpha")
# }