pdb
========================

.. contents::
  :local:

This task is used to obtain a better PDB file. Here "better" meansing correct atom names, residue names, etc., and coordinates into a PBC box.

Arguments
-------------

.. option:: -i, --in

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - Yes
    * - Argument
      - PDB filename or XYZ filename
    * - Default
      - None
  
  Give the input molecule.

.. option:: -t, --top

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - PSF filename
    * - Default
      - None
  
  Give the input topology.

.. option:: -o, --out

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - A filename prefix
    * - Default
      - None
  
  Give the output filename prefix. If not given, the molecule will be written to ``x-pdb.pdb``.

.. option:: --box

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - Three real numbers: x, y, z in Angstrom
    * - Default
      - None
  
  The box size in Angstrom. If given, all coordinates will be moved into this box. A residue will **NOT** be split into two parts.

Here is an example:
  
.. code-block:: bash
  
  $ pdbtop.exe pdb -i mol.xyz -t mol.psf -o mol-sol --box "70 70 70" 

The output ``mol-sol.pdb`` will contain coordinates given in ``mol.xyz`` and topology given in ``mol.psf``. The coordinates will be moved into a box with size 70x70x70 Angstrom, shown below.

.. image:: _static/figs/p13.png