Decomposition analysis¶

Info

This example can be found in the examples/Decomposition_analysis 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`	Receptor and ligand group numbers in the index file
A trajectory file	`xtc` `pdb` `trr`	Final GROMACS MD trajectory, fitted and with no pbc.
Ligand parameters file	`mol2`	The Antechamber output `mol2` file of ligand parametrization
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

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

SerialWith MPIgmx_MMPBSA_test

ggmx_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 -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_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 -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv

gmx_MMPBSA_test -t 14

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

Sample input file for decomposition analysis
Sample input file for decomposition analysis
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="Decomposition",
startframe=1,
endframe=10,
forcefields="leaprc.protein.ff14SB"
/
&gb
igb=5, saltcon=0.150,
/
#make sure to include at least one residue from both the receptor
#and ligand in the print_res mask of the &decomp section.
#this requirement is automatically fulfilled when using the within keyword.
#http://archive.ambermd.org/201308/0075.html
&decomp
idecomp=2, dec_verbose=3,
print_res="within 4"
/

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 with the igb5 (GB-OBC2) model and a salt concentration = 0.15M.

Per-residue decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW potential terms (idecomp=2) is going to be performed and residues within 4Å in both receptor and ligand will be printed in the output file. Please see print_res variable in &decomp namelist variables section.

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. A plain text (FINAL_DECOMP_MMPBSA.dat) and a CSV-format (FINAL_DECOMP_MMPBSA.csv) output files containing all energy terms for each printed residue in decomposition calculations will be also saved.

Important

In several cases, set cartoon_side_chain_helper, 1 in PyMOL causes undesired visual effects, e.g. it shows the terminal chain residue incompletely or hides the oxygen atoms of the PO3 group. Additionally, it can prevent the user from displaying any atoms that are hidden by this method, i.e., the backbone atoms. In such cases, using the command set cartoon_side_chain_helper, 0 should solve teh problem.

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

Alternatives for per-residue energy contribution visualization¶

You can also use VMD and Chimera to view the modified pdb file with the per-residue energy contributions

Last update: November 7, 2023 18:41:32
Created: February 8, 2021 07:10:13