awkwarddna.inp
Page 150.  For inputting a straight pdb of DNA using an unmodified topology file. DNA sequence must be entered into script.

construct.inp
Page 130.  Builds model peptide with Phi and Psi values passed from command line.  Builds alpha-helix, beta-sheet, polyproline helix etc.

correl.inp 
Page 121.  Generates the chi1 and chi2 rotamer angle distributions from a DCD dynamics trajectory.

counter.inp
Page 152. Adds sodium ions halfway between O1P and O2P oxygen atoms on phosphates of DNA.

dimer.inp
Page 64.  Reads in two subunits of a dimeric protein, adds H atoms, adds missing side chain atoms and determines atoms of subunit 1 that lie within 4 Angstroms of any atom of subunit 2.

dmatrix.awk
Page 85.  Used in generating a distance matrix from the output data produced by the coordinate dmat command.

dnainput.inp
Page 149.  General script for inputting pdb files of DNA.  Must first modify pdb with efixpdb.awk, and use modified topology file
top_all27_prot_dna.rtf.
       top_all27_prot_dna.rtf

efixpdb.awk
Page 147.  General script for extracting protein or nucleic acid chains or solvent or ligands from pdb files and modifying them for input to CHARMM.

enrotate.awk
Page 77.  Awk script for translating and rotating molecules in pdb file.  Reports maximum and minimum values of modified x, y, z coordinates.

enrotate.in
Page 78.  CHARMM script for translating and rotating molecules.  Reports maximum and minimum values of modified x, y, z coordinates.

fixpdb.awk
Page 37.  Awk script like efixpdb.awk, but does not handle nucleic acid.

holes.inp
Page 61.  Finds holes in a protein.

inten.inp
Page 117.  Calculates interaction energy between two groups of residues in a protein.

interface.inp
Page 80.  Calculates solvent accessible surface area of a monomer and homodimer so interface area can be calculated.

join.inp
Page 145.  Joins two polypeptide chains with a peptide bond.  Requires the patch join be added to topology file.
    join

langevineef.inp
Page 113.  Runs Langevin dynamics with eef1 implicit water.

mindynb.inp
Page 103. Puts a protein and its crystallographic waters in a water drop, energy minimizes, heats, equilibrates, and performs a dynamics run.

mini.inp
Page 94.  Reads protein.pdb, adds H atoms, adds missing side chain atoms, centers at origin and orients major axis along x axis.

mutate.inp
Page 113.  Mutates a specified residue to another residue.  Segid, residue number to change, and new residue name are specified on command line.

overlay.inp
Page 69.  RMS overlays two proteins utilizing segments of each as specified in the script itself.

periodic.inp
Page 114.  Energy minimizes and heats a system using periodic boundary conditions.

phi.awk
Page 50.  Extracts angle phi from an internal coordinate file.

phipsi.awk
Page 51.  Extracts phi and psi from an internal coordinate file.

readcord.inp
Page 43.  A general shell.  Reads in a protein, adds missing coordinates, writes coordinates, writes psf.

rotadjust.inp
Page 136.  Adjust rotameric states.  At command line specify residue number, four atoms defining a chi angle and new chi value.

rotate.awk
Page 74.  Awk script for translation and rotation.  Fails if no white space between coordinate values.

rotate.inp
Page 75.  Adds missing atoms and then rotates and translates. 

surface.awk
Page 57.  Collects the surface area for each atom in a residue for each residue in a protein in the output from the coordinate surface command.

waterbox.inp
Page 125.  General script for creation of a box of water molelcules.