<h2>CGenFF Force Field Parameterization: Small Molecule Simulation</h2>
<p><a href="https://drive.google.com/drive/u/1/folders/0B2d8Pq0mORNNMm9lclBwak9HYm8" rel="nofollow">Learn More</a></p>
<blockquote>
<p><strong>System Requirements</strong> \
Python with the Numberx package (IVSPLAT2) \
<a href="http://cgenff_charmm2gmx.py" rel="nofollow">cgenff_charmm2gmx.py</a> script file (IVSPLAT2)
1. Open up the ligand.str file in a text editor and note the residue name \
<code>RESI /scrat 0.000 ! param penalty= 228.000 ; charge penalty= 184.921</code>\
<code>BONDS CG2O1 CG2R51 300.00 1.4750 ! /scrat , from CG2O1 CG2R61, penalty= 45</code>
2. Find and replace all “/scrat” or equivalent with a short ligand name, e.g. “3ZM”\
<code>RESI 3ZM 0.000 ! param penalty= 228.000 ; charge penalty= 184.921</code></p>
</blockquote>
