Manual

The following sections briefly describe the method implemented in NMAWRAPPER, how to run NMAWRAPPER from the command-line, the required input and the produced output files.

Introduction

NMAWRAPPER is an utility to compute normal modes of a biological macromolecule. The wrapper calls programs PDBMAT and DIAGRTB in sequence, and write the output to a vectors file.

Running nmawrapper

Usage:

$ nmawrapper [OPTIONS] <COORD FILE>

NMAWRAPPER expects the following command line arguments:

Argument Description
COORD FILE High-resolution atomic model in PDB format.

NMAWRAPPER recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Short Option Long Option Description
-p --prefix=<PREFIX> Prefix to prepend to the output file.
-v --version Print version information and exit.
-h --help Print a summary of arguments, options, and exit.

nmawrapper Input Files

NMAWRAPPER expects atomic coordinates in Protein Data Bank (PDB) format.

nmawrapper Output Files

The vectors file generated as output contains the normal modes (eigenvalues and eigenvectors) in the format used by DIAGTRB.