Read AMBER Coordinate files
Read coordinate data from an AMBER coordinate / restart file.
## S3 method for class 'amber' read.crd(file, ...)
file |
name of crd file to read. |
... |
arguments passed to and from functions. |
Read a AMBER Coordinate format file.
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. |
See AMBER documentation for Coordinate format description.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. http://ambermd.org/FileFormats.php
## 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")
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