read.prmtop: Read AMBER Parameter/Topology files

In bio3d: Biological Structure Analysis

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: https://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.

Note

See AMBER documentation for PrmTop format description:
https://ambermd.org/FileFormats.php.

Author(s)

Lars Skjaerven

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. https://ambermd.org/FileFormats.php

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)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.