Tutorial 5: Get A Better PDB File
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.. contents::
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In this tutorial, we will show you how to use pdbtop to treat PDB and XYZ files to a better format.

Using PSF Information
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Sometime you have an XYZ file (maybe obtained from a MD simulation) that does not have information like atom names, residue names, etc. You can use the PSF file to correct them. The following example will show you how to do that.

.. code-block:: bash

  $ pdbtop pdb -i d5-final.xyz -t d5.psf -o d5-final

Then, in ``d5-final.pdb``, you will see correct atom names etc. It also works for PDB files.

Wrapping Molecules into a box
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In a MD simulation with periodic boundary condition, the coordinates of a molecule may be outside the box. You can use the following command to wrap them into a box.

.. code-block:: bash

  $ pdbtop pdb -i d5-final.xyz -t d5.psf -o d5-pbc --box "70 70 70" # or "-i d5-final.pdb", both works
  
A good point is that a residue will **NOT** be split into two parts. The results are shown below:

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