inate.
<p>
<hr align="center"/>
<p> 
<h3><a name="tools">Setting up the simulation with individual tools</a></h3>
In this advanced section we will go through the setup of the simulations step-by-step using individual setup scripts rather than <code>protoms.py</code>. This is relevant in cases where you are interested in specifying certain parameters which are pre-determined by <code>protoms.py</code>.
<h5>Setting up the ligand</h5>
We will start setting up the ligand from the initial <code>fragment.pdb</cod