Binding free energy calculation with GBNSR6 model¶

Info

This example can be found in the examples/GBNSR6 directory in the repository folder. If you didn't use gmx_MMPBSA_test before, use downgit to download the specific folder from gmx_MMPBSA GitHub repository.

Requirements¶

In this case, gmx_MMPBSA requires:

Input File required	Type	Description
Input parameters file	`in`	Input file containing all the specifications regarding the type of calculation that is going to be performed
The MD Structure+mass(db) file	`tpr` `pdb`	Structure file containing the system coordinates
An index file	`ndx`	File containing the receptor and ligand in separated groups
Receptor and ligand group	`integers`	Group numbers in the index files
A trajectory file	`xtc` `pdb` `trr`	Final GROMACS MD trajectory, fitted and with no pbc.
A topology file	`top`	GROMACS topology file (The `* .itp` files defined in the topology must be in the same folder
A Reference Structure file	`pdb`	Complex reference structure file (without hydrogens) with the desired assignment of chain ID and residue numbers

-> 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:

SerialWith MPI

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

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

Sample input file for GB calculation using GBNSR6 model
Sample input file for GB calculation using GBNSR6 model
#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="GBNSR6",
startframe=1,
endframe=10,
forcefields="leaprc.protein.ff14SB"
/

&gbnsr6
istrng=0.15
/

Keep in mind

See a detailed list of all the options in gmx_MMPBSA input file here as well as several examples. These examples are meant only to show that gmx_MMPBSA works. It is recommended to go over these variables, even the ones that are not included in this input file but are available for the calculation that it's performed and see the values they can take (check the input file section). This will allow you to tackle a number of potential problems or simply use fancier approximations in your calculations.

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.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, 10 frames are going to be used when performing the MM/PB(GB)SA calculation using the GBNSR6 model.

Comments on GBNSR6 model

GBNSR6 is an implementation of the Generalized Born (GB) model in which the effective Born radii are computed numerically, via the so-called "R6" integration (ref.) over molecular surface of the solute.
In contrast to most GB practical models, GBNSR6 model is parameter free in the same sense as the numerical PB framework is. Thus, accuracy of GBNSR6 relative to the PB standard is virtually unaffected by the choice of input atomic radii.
Check Chapter §5 in Amber manual for a more thorough description of the GBNSR6 model and its parameters.

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.

Note

Once the calculation is done, the results can be analyzed in gmx_MMPBSA_ana (if -nogui flag was not used in the command-line). Please, check the gmx_MMPBSA_ana section for more information.

Last update: February 21, 2023 01:10:05
Created: October 17, 2020 22:35:03