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Read coordinate data from an AMBER coordinate / restart file.
# S3 method for amber
read.crd(file, ...)A list object of type ‘amber’ and ‘crd’ with the following components:
a numeric matrix of class ‘xyz’ containing the Cartesian coordinates.
a numeric vector containg the atom velocities.
numeric, length of the simulation (applies to Amber restart coordinate files).
total number of atoms in the coordinate file.
dimensions of the box.
name of crd file to read.
arguments passed to and from functions.
Lars Skjaerven
Read a AMBER Coordinate format file.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. http://ambermd.org/FileFormats.php
read.prmtop, read.ncdf,
as.pdb, atom.select,
read.pdb, read.crd.charmm
if (FALSE) {
## 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")
}
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