Read AMBER Parameter/Topology files
Read parameter and topology data from an AMBER PrmTop file.
read.prmtop(file) ## S3 method for class 'prmtop' print(x, printseq=TRUE, ...)
file |
a single element character vector containing the name of the PRMTOP file to be read. |
x |
a PRMTOP structure object obtained from
|
printseq |
logical, if TRUE the residue sequence will be printed
to the screen. See also |
... |
additional arguments to ‘print’. |
This function provides basic functionality to read and parse a AMBER PrmTop file. The resulting ‘prmtop’ object contains a complete list object of the information stored in the PrmTop file.
See examples for further details.
Returns a list of class ‘prmtop’ (inherits class ‘amber’) with components according to the flags present in the PrmTop file. See the AMBER documentation for a complete list of flags/components: http://ambermd.org/FileFormats.php.
Selected components:
ATOM_NAME |
a character vector of atom names. |
ATOMS_PER_MOLECULE |
a numeric vector containing the number of atoms per molecule. |
MASS |
a numeric vector of atomic masses. |
RESIDUE_LABEL |
a character vector of residue labels. |
RESIDUE_RESIDUE_POINTER |
a numeric vector of pointers to the first atom in each residue. |
call |
the matched call. |
See AMBER documentation for PrmTop format description:
http://ambermd.org/FileFormats.php.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. http://ambermd.org/FileFormats.php
## Not run:
## Read a PRMTOP file
prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))
print(prmtop)
## Explore prmtop file
head(prmtop$MASS)
head(prmtop$ATOM_NAME)
## Read Amber coordinates
crds <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))
## Atom selection
ca.inds <- atom.select(prmtop, "calpha")
## Convert to PDB format
pdb <- as.pdb(prmtop, crds)
pdb.ca <- as.pdb(prmtop, crds, inds=ca.inds)
## Trajectory processing
#trj <- read.ncdf("traj.nc", at.sel=ca.inds)
## Convert to multimodel PDB format
#pdb <- as.pdb(prmtop, trj[1:20,], inds=ca.inds, inds.crd=NULL)
## RMSD of trajectory
#rd <- rmsd(crds$xyz[ca.inds$xyz], traj, fit=TRUE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.