Read Coordinate Data from Amber or Charmm

Usage

read.crd(file, ...)

Arguments

file
the name of the coordinate file to be read.
...
additional arguments passed to the methods read.crd.charmm or read.crd.amber.

Description

Read a CHARMM CARD (CRD) or AMBER coordinate file.

Details

read.crd is a generic function calling the corresponding function determined by the class of the input argument x. Use methods("read.crd") to get all the methods for read.crd generic:

read.crd.charmm will be used for file extension ‘.crd’.

read.crd.amber will be used for file extension ‘.rst’ or ‘.inpcrd’.

See examples for each corresponding function for more details.

Value

See the ‘value’ section for the corresponding functions for more details.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

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





## Read a Amber CRD file
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, 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

See also

read.crd.amber, read.crd.charmm, write.crd, read.prmtop, read.pdb, write.pdb, atom.select, read.dcd, read.ncdf

Author

Barry Grant and Lars Skjaerven