
This directory contains example proteins for use with VMD.  

Some brief descriptions:

alanin -- a simple (66 atom) system.  
  files: alanin.pdb alanin.psf alanin.dcd alanin2.dcd 
  The pdb file determines the coordinates.  The psf determines the 
  bond topology (but is optional), and the dcd files are binary trajectory 
  formats common to CHARMm, XPlor, and NAMD.  One is in little-endian 
  format, the other is in big-endian format.

bacteriorhodopsin (brH) -- a realistic system ; 
  files: brH.pdb brH.psf
People here did research on it.  This has about 4,000 atoms.  The special
parts of it are "resid 216" (or "resname LYR") and "water".
Please contact us about using this structure in anything other
than educational purposes.

Others:
  The three files "deoxy", "mbco" and "star" are different
states of myoglobin contributed by Joel Berendzen (see Nature,
v. 371, Oct. 27, 1994, p808).  We modified the files somewhat
so they all have the same number of atoms in the structure.

Bovine trypsin inhibitor (IIRC)
  files: bpti.pdb  

A small DNA section we created by truncating a larger structure
  files: dna.pdb dna.psf

Enjoy,
  The VMD Developers
  vmd@ks.uiuc.edu
  October 29, 2001
