NAME

peptide - generate a peptide from a structure type and sequence

SYNOPSIS

peptide [-outf string] [-lib string] -stype string -seq string
[-help] [-usage]

DESCRIPTION

peptide is an nab program, originally written by Paul Beroza, that
will generate a pdb file given a structure type and a
sequence. You must have the nab compiler (part of AmberTools):
http://ambermd.org/

Once you have the nab compiler installed, you can compile peptide:

 % make

The Makefile should work with most Unix make programs (tested using
the FreeBSD Berkeley make and gmake). You should edit the Makefile
to change the variables to suit your local environment.

 % make install

will install the program.

The command line syntax for peptide is:

 % peptide -stype structure -seq sequence [-lib libfile] [-o outfile]

where "structure" defines the type of structure to be created and
"sequence" is a string of one letter amino acid codes. The -stype and
-seq options are required. By default peptide writes to stdout. For
example:

 % peptide -stype ALPHA -seq AAAAA

will create an alpha helical alanine pentapeptide.

The options also have single character versions: -l for -lib, -o for
-outfile, -t for -stype and -s for -seq. The multicharacter options
may be introduced with -- instead of - and -? is synonymous with
-help. An alternative syntax is also available: -outfile=afile is
accepted instead of the -outfile afile construct; see the man page
for getopt_long(3).

The structure definitions are stored in a library file that can be specified
on the command line (the "-lib libfile" option) or by default are taken
from $NABHOME/reslib/conf.lib.

A sample library "conf.lib" is included. 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 is one, 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 us know of any bugs or suggestions.

Original version by Paul Beroza <pberoza@telik.com>

Modified by M. L. Dodson <activesitedynamics@comcast.net> to add
command line parsing using getopt_long, a generic Makefile, and
conversion of the README to a man page.

COPYRIGHT AND LICENSE

Originally created by Paul Beroza. Please see the COPYING file in the
AmberTools distribution for information on copyright and license
issues.
