Protein-protein binding free energy calculations (Single Trajectory method) with OPLSff files¶

Requirements¶

In this case, gmx_MMPBSA requires:

-> Must be defined -- -> Optional, but recommended -- -> Optional

See a detailed list of all the flags in gmx_MMPBSA command line here

Command-line¶

That being said, once you are in the folder containing all files, the command-line will be as follows:

gmx_MMPBSA -O -i mmpbsa.in -cs com.pdb -ct com_traj.xtc -ci index.ndx -cg 10 11 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.pdb -ct com_traj.xtc -ci index.ndx -cg 10 11 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

where the mmpbsa.in input file, is a text file containing the following lines:

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Sample input file for PB calculation
#This input file is meant to show only that gmx_MMPBSA works. 
Although, we tried to use the input files as recommended in the
#Amber manual, some parameters have been changed to perform 
more expensive calculations in a reasonable amount of time. 
Feel free to change the parameters #according to what is better 
for your system.

&general
sys_name="OPLS_Support",
startframe=1,
endframe=8,
/
&pb
radiopt=0, istrng=0.150,
/

See a detailed list of all the options in gmx_MMPBSA input file here as well as several examples

Considerations¶

In this case, a single trajectory (ST) approximation is followed, which means the receptor and ligand structures and trajectories will be obtained from that of the complex. To do so, an MD Structure+mass(db) file (com.pdb), an index file (index.ndx), a trajectory file (com_traj.xtc), and both the receptor and ligand group numbers in the index file (10 11) are needed. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. In this case, 8 frames are going to be used when performing the MM/PB(GB)SA calculation with the PB model (linear PB equation) and a salt concentration = 0.15M.

A plain text output file with all the statistics (default: FINAL_RESULTS_MMPBSA.dat) and a CSV-format output file containing all energy terms for every frame in every calculation will be saved. The file name in '-eo' flag will be forced to end in [.csv] (FINAL_RESULTS_MMPBSA.csv in this case). This file is only written when specified on the command-line.