bio3d (version 2.3-3)

read.prmtop: Read AMBER Parameter/Topology files

Description

Read parameter and topology data from an AMBER PrmTop file.

Usage

read.prmtop(file)
# S3 method for prmtop
print(x, printseq=TRUE, …)

Arguments

file

a single element character vector containing the name of the PRMTOP file to be read.

x

a PRMTOP structure object obtained from read.prmtop.

printseq

logical, if TRUE the residue sequence will be printed to the screen. See also pdbseq.

...

additional arguments to ‘print’.

Value

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/formats.html.

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.

Details

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.

References

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

See Also

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

Examples

# 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)
# }