Charmm Cgenff, Small Molecule

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<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>
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