Sample input file for GB calculationThis input file is meant to show only that gmx_MMPBSA works. Althought,we tried to used the input files as recommended in the Amber manual,some parameters have been changed to perform more expensive calculationsin a reasonable amount of time. Feel free to change the parameters according to what is better for your system.&generalsys_name="Prot-Prot",startframe=5,endframe=14,forcefields="oldff/leaprc.ff99SB",/&gbigb=2, saltcon=0.150,/
In this case, a single trajectory (ST) approximation is followed, which means the receptor and ligand (in this case, the ligand is also another protein) amber format topologies and trajectories will be obtained from that of the complex. To do so, an MD Structure+mass(db) file (com.tpr), an index file (index.ndx), a trajectory file (com_traj.xtc), and both the receptor and ligand group numbers in the index file (19 20) are needed. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. In this case, 10 frames are going to be used when performing the MM/PB(GB)SA calculation with the igb2 (GB-OBC1) model and a salt concentration = 0.15M.
