# Name for the protocol
Name: MMGBSA ranking from 20 MD replicates 
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# All software packages used and their versions:
Software: AMBER14
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# List any number of key computational parameters in the following lines:
Parameters: Assumed pH 7.4
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# Provide free text description of your method below. Use as many lines as you need. 
Method: 
1. Starting structure:  Protein PDB files were prepared by Ying/Deping/Hongwu with filled missing loops. Ligand docking structures were prepared by Xevi with Glide XP with the confident pose.
2. MD simulation: Use AMBER14 to equilibrate the protein-ligand complex starting structure for 5 ns, then run additional 20 replicates with 5ns each  by restarting from the identical equilibrated atomic coordinates but different initial velocities generated from a Maxwell-Boltzmann distribution. 
3. Ranking Score: The last 1.5 ns of each replicate was used as the production, which generated 300 snapshots in total. AMBER MMGBSA method was used to analyze the total free energy. Entropy contribution was not included.

