read.prmtop. bio3d 2.3-0

Usage

read.prmtop(file)
"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’.

Description

Read parameter and topology data from an AMBER PrmTop file.

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

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.

References

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

Note

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

Examples

## Read a PRMTOP file
prmtop <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))
print(prmtop)


 Call:
  read.prmtop(file = system.file("examples/crambin.prmtop", package = "bio3d"))

 Class:
  amber, prmtop

 System information: 
      Total number of atoms:  639
      Solute residues:  46
      Solute molecules:  1

 Sequence:
      TTCCPSIVARSNFNVCRLPGTSEAICATYTGCIIIPGATCPGDYAN



## Explore prmtop file
head(prmtop$MASS)

[1] 14.010  1.008  1.008  1.008 12.010  1.008

head(prmtop$ATOM_NAME)

[1] "N"  "H1" "H2" "H3" "CA" "HA"


## Read Amber coordinates
crds <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))

## Atom selection
ca.inds <- atom.select(prmtop, "calpha")


 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..       46 atom(s) from 'string' selection 
 ..       46 atom(s) in final combined selection 

 .. number of atoms in PDB:  639 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46 



## Convert to PDB format
pdb <- as.pdb(prmtop, crds)


 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..       46 atom(s) from 'string' selection 
 ..       46 atom(s) in final combined selection 

 .. number of atoms in PDB:  639 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46 


pdb.ca <- as.pdb(prmtop, crds, inds=ca.inds)


 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..       46 atom(s) from 'string' selection 
 ..       46 atom(s) in final combined selection 

 .. number of atoms in PDB:  46 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46 



## 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)

Author

Lars Skjaerven

Read AMBER Parameter/Topology files