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 $AMBERHOME/dat/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 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 may be of any length. For other structure types, the number of residues in 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 Modified by M. L. Dodson 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.