# Name for the protocol
Name: MMPBSA
#
# All software packages used and their versions:
Software: AMBER11
#
# List any number of key computational parameters in the following lines:
Parameters: AM1-bcc #atomic charges for ligands
Parameters: AMBER03 force field
Parameters: Generalized Amber force field (GAFF)
Parameters: 3 ns
Parameters: exdi = 80
Parameters: indi = 1
#
# Provide free text description of your method below. Use as many lines as you need. 
Method: For each ligand, the initial structure was generated with the XDZ_0 method, 
as described in the PosePredictionProtocol. Molecular Dynamics simulations and free 
energy calculations using MM/PBSA method were conducted to calculate the free energy 
of binding. Specifically, the temperature of the prepared complex system was raised 
from 0 to 300k in the heating phase. Then, the production phase was performed for 3ns 
at a time step of 2 fs. To obtain the free energy of binding, 1500 snapshots were taken 
from the last 1.5ns at the 1 ps interval and calculated by implementing the MM/PBSA method. 
Entropical loss during protein-ligand binding was estimated by employing the Nmode module 
in the AMBER package based on the 50 snapshots extracted from the last 1.5ns with the 30 ps interval.

