R: Read AMBER Parameter/Topology files

read.prmtop {bio3d} | R Documentation

## Read AMBER Parameter/Topology files

### Description

Read parameter and topology data from an AMBER PrmTop file.

### Usage

    read.prmtop(file)

    ## S3 method for class '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’.

### 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.

### 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.

### Note

See AMBER documentation for PrmTop format description:
http://ambermd.org/formats.html.

### Author(s)

Lars Skjaerven

### 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)

    ## End(Not run)

[Package bio3d version 2.3-3 Index]