
<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>
<h5>Setting up the free leg</h5>
We will start setting up the free-leg simulation. However, it should be noted that some of the files created in this section will also be used in the bound-leg simulation.
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<li>First we need to make sure that the very first line of lig1.pdb 