nmawrapper
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
Command-Line
Usage:
$ nmawrapper [OPTIONS] <COORD FILE>
NMAWRAPPER expects the following command line arguments:
Arguments and Options
| 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 accepts atomic coordinate data in .pdb format as input. This may be either a relative or absolute file path, or data will be read from stdin.
nmawrapper Output Files
The vectors file generated as output contains the normal modes (eigenvalues and eigenvectors) in the format used by DIAGTRB.