.. |g_mmpbsa publication| raw:: html
g_mmpbsa publication
Binding energy calculation
==========================
Download Tutorial Package
--------------------------
To download the tutorial package, click on this `link `_.
This package contains required file for the tutorial.
Untar this package by following command:
::
tar -zxvf tutorial.tar.gz
cd tutorial
cd 1EBZ
This directory contains topology-parameter (``tpr``),
atom-index (``ndx``), and trajectory (``xtc``) files of a HIV-1 protease inhibitor complex.
Calculation of three energy components
--------------------------------------
The binding energy consists of three energetic terms,
(a) potential energy in vacuum,
(b) polar-solvation energy and
(c) non-polar solvation energy.
These energetic terms could be calculated in either three or one step.
Three steps calculation
------------------------
1. Calculation of potential energy in Vacuum
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execute the following command:
::
g_mmpbsa run -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -pdie 2 -decomp -unit1 Protein -unit2 BEC
Here we are selecting ``Protein`` as unit-1 and ``BEC``, which is a ligand, as unit-2. The binding
energy will be calculated between the protein and ligand.
Two files ``energy_MM.xvg`` and ``contrib_MM.dat`` are generated as outputs.
Both files could be generated with different name by
``-mm filename1.xvg`` and ``-mmcon filename2.dat``.
``energy_MM.xvg`` file contains van der Waals, electrostatic interactions, and net non-bonded potential
energy between the protein and inhibitor.
``contrib_MM.dat`` contains contribution of each residue to the calculated net
non-bonded interaction energy.
2. Calculation of polar solvation energy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
To calculate the polar solvation energy, an input file (e.g. tutorial/polar.mdp) is required.
This file contains input parameters that are used in the calculation of polar solvation energy.
.. note:: `Please click here for details about polar solvation input parameters <../parameters/polar-parameters.html>`_.
Execute the following command:
::
g_mmpbsa run -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../polar.mdp -nomme -pbsa \
-decomp -unit1 Protein -unit2 BEC -pol polar.xvg -pcon contrib_pol.dat
Two files ``polar.xvg`` and ``contrib_pol.dat`` are generated as outputs.
Both files could be generated with different name by ``-pol filename1.xvg``
and ``-pcon filename2.dat``.
``polar.xvg`` contains polar solvation energies for unbound protein, unbound inhibitor
and protein-inhibitor complex.
``contrib_pol.dat`` contains contribution of each residue to the calculated net polar
solvation energy.
3. Calculation of non-polar solvation energy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
To calculate the non-polar solvation energy, an input file (e.g. tutorial/apolar_sasa.mdp)
is required. This file contains parameters that are used in the calculation of non-polar
solvation energy.
There are several type of non-polar models that are discussed in the |g_mmpbsa publication|.
Here, SASA-only and SAV-only model are used for which input parameter files are provided.
.. note:: `Please click here for details about non-polar solvation input parameters <../parameters/non-polar-parameters.html>`_.
.. warning:: Now WCA model is removed from the g_mmpbsa package.
**For SASA-only model:**
Execute the following command:
::
g_mmpbsa run -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../apolar_sasa.mdp -nomme -pbsa -decomp \
-unit1 Protein -unit2 BEC -apol sasa.xvg -apcon sasa_contrib.dat
Two files ``sasa.xvg`` and ``sasa_contrib.dat`` are generated as outputs.
``sasa.xvg`` contains non-polar solvation energy for unbound protein,
unbound inhibitor and protein-inhibtor complex. ``sasa_contrib.dat``
contains contribution of each residue to the calculated net polar-solvation energy.
**For SAV-only model:**
Execute the following command:
::
g_mmpbsa run -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../apolar_sav.mdp -nomme -pbsa -decomp \
-unit1 Protein -unit2 BEC -apol sav.xvg -apcon sav_contrib.dat`
Two files ``sav.xvg`` and ``sav_contrib.dat`` are generated as outputs.
``sav.xvg`` contains non-polar solvation energy for unbound protein,
unbound inhibitor and protein-inhibtor complex. ``sav_contrib.dat``
contains contribution of each residue to the calculated net polar-solvation energy.
One step calculation
--------------------
Execute the following command:
::
g_mmpbsa run -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../pbsa.mdp -pdie 2 -pbsa -decomp \
-unit1 Protein -unit2 BEC -os energy_summary.csv \
-ores residues_energy_summary.csv -silent
Here we are selecting ``Protein`` as unit-1 and ``BEC``, which is a ligand, as unit-2. The binding
energy will be calculated between the protein and ligand.
``pbsa.mdp`` contains input parameters for both polar and SASA-only non-polar solvation energies.
All three energetic terms are calculated by using the above single command and all output files
are generated.
``-os energy_summary.csv``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
It will also calculate average binding energy and standard deviation of all the energy terms
and will be output in **CSV format** ``energy_summary.csv`` file provided with ``-os`` option.
This file can be directly opened in MS excel or any other spreadsheet software.
::
"Energy" , "Average", "Standard-Deviation",
"vDW" , -334.587 , 15.897,
"Electrostatic" , -318.759 , 32.401,
"Polar-solvation" , 313.703 , 10.426,
"Non-polar-solvation", -30.420 , 1.016,
"Total" , -370.062 , 32.903,
``-ores residues_energy_summary.csv``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This file contain summary of binding energy contributions (both average and standard deviation)
of residues over all frames.
The output file has following rows and columns:
::
"Residue", "vDW" , "vdW-stddev", "Elec." , "Elec.-stdev", "polar", "polar-stdev", "apolar", "apolar-stdev", "total" , "total-stdev",
"PRO-1" , -0.004 , 0.001, 0.655 , 0.660, -0.202 , 0.186, 0.000 , 0.000, 0.449 , 0.520,
"GLN-2" , -0.005 , 0.000, 0.094 , 0.074, -0.112 , 0.060, 0.000 , 0.000, -0.023 , 0.032,
"ILE-3" , -0.018 , 0.003, -0.083 , 0.035, 0.101 , 0.025, 0.000 , 0.000, -0.000 , 0.029,
"THR-4" , -0.014 , 0.001, -0.013 , 0.073, 0.004 , 0.044, 0.000 , 0.000, -0.022 , 0.062,
"LEU-5" , -0.078 , 0.009, 0.169 , 0.061, -0.015 , 0.056, 0.000 , 0.000, 0.076 , 0.055,
"TRP-6" , -0.039 , 0.005, 0.164 , 0.056, 0.009 , 0.025, 0.000 , 0.000, 0.134 , 0.052,
"GLN-7" , -0.068 , 0.014, -0.211 , 0.152, 0.238 , 0.086, 0.000 , 0.000, -0.040 , 0.132,
"ARG-8" , -5.167 , 1.695, -3.454 , 4.016, 9.184 , 4.154, -0.637 , 0.191, -0.074 , 3.831,
"PRO-9" , -0.202 , 0.041, -0.029 , 0.120, 0.076 , 0.072, 0.000 , 0.000, -0.155 , 0.122,
"LEU-10" , -0.196 , 0.057, -0.046 , 0.061, 0.034 , 0.027, 0.000 , 0.000, -0.208 , 0.077,
.
.
.
Average Binding Energy Calculation
----------------------------------
The average binding energies can be directly calculated in one-step method as described above.
However, the bootstrap analysis could be used to calculate the average binding energy with standard error.
To calculate average binding energy, execute following command:
::
g_mmpbsa average -m energy_MM.xvg -p polar.xvg -a apolar.xvg -bs
Three output files ``full_energy.dat``, ``summary_energy.dat`` and
``summary_energy.csv`` are obtained. Both ``summary_energy.dat`` and ``summary_energy.csv``
contains average and standard deviations of all energetic components
including the binding energy as follows:
::
#Complex Number: 1
===============
SUMMARY
===============
van der Waal energy = -334.587 +/- 15.514 kJ/mol
Electrostattic energy = -159.380 +/- 15.810 kJ/mol
Polar solvation energy = 313.698 +/- 10.174 kJ/mol
SASA energy = -30.431 +/- 0.996 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = -210.699 +/- 19.745 kJ/mol
===============
END
===============
``full_energy.dat`` contains the values of energetic terms as a function of time.
Last four columns contains Δ_E_MM, Δ_G_polar, Δ_G_nonpolar and Δ_G_binding
as a function of time. These quantities could be plotted with xmgrace/matplotlib/gnuplot.
The respective four files in xmgrace format (_agr_) are provided in `tutorial/1EBZ/output`
.. image:: ../_static/images/binding_energy.png
.. image:: ../_static/images/Emm_energy.png
.. image:: ../_static/images/polar_energy.png
.. image:: ../_static/images/nonpolar_energy.png
To calculate average binding energy by using bootstrap analysis, execute following command:
::
g_mmpbsa run -bs -nbs 2000 -m energy_MM.xvg -p polar.xvg -a apolar.xvg
Again, two output files ``full_energy.dat`` and ``summary_energy.dat`` are generated as outputs.
``full_energy.dat`` is similar to that of the above one.
However, ``summary_energy.dat`` contains average and standard error of all energetic components
including the binding energy.
Average values in ``summary_energy.dat`` are slightly different from the above one.
For more details about this method, please follow the |g_mmpbsa publication|.