Tutorial 4: Modifications and Mutations
========================================

.. contents::
  :local:

In this tutorial, we will show you how to use pdbtop to modifications or mutations.

Before any mutations or modifications, you have to have 2 files: pdb and psf. So, please read :doc:`tutorial-1` first.

.. hint::

  For all supported modifications, please refer to the :doc:`modify` page.  

Modifications
--------------------------

Assume we have a protein structure ``5vbm-4.pdb`` and its topology ``5vbm-4.psf`` (see :doc:`tutorial-1`), and we want to perform an "asymmetric dimethylation" for the residue Arg41 at chain A, then we can use the following command:

.. code-block:: bash

  $ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-arg41 --adma 41A

Now we check the result:

.. image:: _static/figs/p12.png

Mutations
--------------------------

To mutate, say, Arg41 to Serine, we can use the following command:

.. code-block:: bash

  $ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-a41s --mutate "41A SER"

Now we check the result:

.. image:: _static/figs/p11.png

You can do multiple mutations at once, like:

.. code-block:: bash

  $ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-6 --mutate "41A SER 45A ALA"