Correlation¶

Info

This example can be found in the examples/Correlation 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 will be run for each system and requires for each of them:

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`	Receptor and ligand group numbers in the index file
A trajectory file	`xtc` `pdb` `trr`	Final GROMACS MD trajectory, fitted and with no pbc.
A topology file (not included)	`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, use bash to loop over the folder and run the calculation in each one of them:

for i in */
>do 
>echo $i
>cd $i
>gmx_MMPBSA -O -i mmpbsa.in -cs ../com.tpr -ci ../index.ndx -cg 20 21 -ct ../com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui
>cd ..
>done

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 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 (20 21) are needed. . As we are running a GB calculation for the wild-type and the mutants, we can use the same MD Structure+mass(db) (../com.tpr), index (../index.ndx), and the trajectory file (../com_traj.xtc) for all systems. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation and will be specific for each mutant, indicating the mutation and the experimental Ki. In this case, 10 frames are going to be used when performing the MM/PB(GB)SA calculation with the igb8 (GB-Neck2) model and a salt concentration = 0.15M. Of note, mbondi3 radii (PBRadii=4) will be used as recommended for GB-Neck2 solvation model.

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 for each system.

Correlation analysis with `gmx_MMPBSA_ana`¶

Once the calculation is done, the results can be analyzed in gmx_MMPBSA_ana. For correlation analysis, gmx_MMPBSA_ana can load the system recursively from the folders with the following command-line:

gmx_MMPBSA_ana -r

The following video shows how to perform correlation analysis in gmx_MMPBSA_ana.

Last update: February 21, 2023 00:52:42
Created: February 8, 2021 07:10:13