Protein-protein binding free energy calculations with MM/3D-RISM¶

Requirements¶

In its simplest version, 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.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

gmx_MMPBSA_test -t 18

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

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Sample input file for MM/3D-RISM
This 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 calculations
in a reasonable amount of time. Feel free to change the parameters 
according to what is better for your system.

&general
sys_name="3D-RISM",
startframe=5,
endframe=8,
/
&rism
polardecomp=0, tolerance=0.001, rism_verbose=2, closure="kh"
/

Considerations¶

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 (3 4) are needed. The mmpbsa. in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. In this case, 4 frames are going to be used when performing the MM/PB(GB)SA calculation with the 3D-RISM model using Kovalenko-Hirata clousure with a 0.001. Note that we have increased the tolerance from 0.00001 (default) to 0.001 in order to reduce the computation time.

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.