"peptide" is an nab program that will generate a pdb file given a structure
type and a sequence.  It was created by Paul Beroza.
Please see the COPYING file for information on copyright and license issues.

You must have the "nab" compiler:
  info on nab = http://www.scripps.edu/case.
  nab source  = ftp://ftp.scripps.edu/pub/macke/nab-3.0.tar.gz (or later)

Once you have the nab compiler installed, can can compile peptide with the
enclosed Makefile by typing make in the directory with the source files.

The command line syntax for peptide is:

% peptide  structure sequence [ -lib libfile ]

where "structure" defines the type of structure to be created and "sequence"
is a string o of 1 letter amino acid codes.  For example:

% peptide ALPHA  AAAAA -lib conf.lib

will create and alanine pentapeptide in an alpha helical structure.

The structure definitions are stored in a library file that can be specified
on the command line  (the "-lib libfile" option) or from the environment
variable "PEPLIB"

I've included a sample library  "conf.lib" This file looks like:

--------------------
ALPHA  1 	alpha helix
phi    -57.0 psi    -47.0 omega  180.0

ABETA 1 	anti-parallel beta sheet
phi    -139.0 psi    135.0 omega  -178.0
	.
	.
	.etc.
--------------------

The file contains sets of definitions, one for each structure type.  The
definitions above are separated by a blank line, but that is not necessary.
Each time peptide finds a line that begins with an alphanumeric character,
it initializes a new structure type with the first string in the line as its
identifying string.  The <structure> on the command line must match one of
the structure types in the "conf.lib" file.

The next field on the structure type line is the number of residues in the
structure.  The following lines must contain the phi psi and omega values
for each of the residues in the structure type.  The angles may be in any
order, but the string defining the angle must precede its floating point
value.

If the number of residues = 1, it is a special structure for which the phi
psi and omega values are the same for all residues in the structure.  For
these structure types, the <sequence> may be of any length.  For other
structure types, the number of residues in <sequence> must agree with the
number of residues in the corresponding structure type in the "conf.lib"
file.  The resulting pdb file is written to standard out.

Please let me know of any bugs or suggestions.

Enjoy,

Paul Beroza  <pberoza@info.combichem.com>
