MM/PBSA method for GROMACS.
This project is maintained by RashmiKumari
g_mmpbsa calculates binding energy of biomolecular associations like protein-protein, protein-ligand protein-DNA etc using MM-PBSA. It gives the different component of energy term in separate file so that user will have choice to have either MM, PB and SA energy values or all energies according to their objective. The tool also gives residue wise contribution to total binding energy which will provide information about important contributing residues to the molecular association.
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Run input file: tpr tpb tpa
-i grompp.mdp Input, Opt. grompp input file with MD parameters
-n index.ndx Input, Opt. Index file
-mm energy_MM.xvg Output, Opt. xvgr/xmgr file
-pol polar.xvg Output, Opt. xvgr/xmgr file
-apol apolar.xvg Output, Opt. xvgr/xmgr file
-mmcon contrib_MM.dat Output, Opt. Generic data file
-pcon contrib_pol.dat Output, Opt. Generic data file
-apcon contrib_apol.dat Output, Opt. Generic data file
Option Type Value Description
------------------------------------------------------
-[no]h bool yes Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]silent bool no Display messages, output and errors from external
APBS program. Only works with external APBS
program
-rad enum bondi van der Waal radius type: bondi, mbondi, mbondi2
or amber
-rvdw real 1 Default van der Waal radius (in nm) if not found
-[no]mme bool yes To calculate vacuum molecular mechanics energy
-pdie real 1 Dielectric constant of solute. Should be same as
of polar solvation
-[no]incl_14 bool no Include 1-4 atom-pairs, exclude 1-2 and 1-3 atom
pairs during MM calculation. Should be "yes" when
groups are bonded with each other.
-[no]focus bool no To enable focusing on the specfic region of
molecule, group of atoms must be provided in
index file
-[no]pbsa bool no To calculate polar and/or non-polar solvation
energy
-ndots int 24 Number of dots per sphere in the calculation of
SASA, more dots means more accuracy
-[no]diff bool yes Calculate the energy difference between two group
otherwise only calculates for one group
-[no]decomp bool no Decomposition of energy for each residue
-s topol.tpr
Input tpr/tpx file of molecule.
-f traj.xtc
Input trajectory xtc/trr format file.
WARNING: Trajectory should be PBC corrected and molecule should not be PBC broken. To make molecule whole in trajectory, please follow these links: PBC and trjconv.
-n index.ndx
Input atomic index file. User will get choice to select atomic groups.
-i mmpbsa.mdp
Input parameter file for polar and non-polar solvation energy. For more details about accepted keywords and options, follow these two links: Polar-Solvation Keywords and Non-polar Solvation Keywords.
-mm energy_MM.xvg
van der Waal and electrostatic energy of the selected atom group/s.
With -nodiff option, only one index group can be selected. In this case, this file contains vacuum MM energy of this selected group. Always USE -incl_14 option for single group calculations.
By default, two groups can be selected, and this file contains only interaction energy between two groups. Energy of each group and thier complex is not calculated.
However, with -incl_14 option, vacuum MM energy componenets for each group and their complex is calculated. Interaction energy can be calculated later using the provided Python scripts.
-pol polar.xvg
Polar solvation energy of the selected atoms group/s.
With -nodiff option, only one index group can be selected. In this case, this file contains energy of this selected group.
By default, two groups can be selected, and this file contains energy of each group and thier complex.
-apol apolar.xvg
Non-polar solvation energy of the selected atoms group/s.
With -nodiff option, only one index group can be selected. In this case, this file contains energy of this selected group.
By default, two groups can be selected, and this file contains energy of each group and thier complex.
-mmcon contrib_MM.dat
Vacuum MM van der Waals and electrostatic energy contribution per residue per frame/snaspshot.
-pcon contrib_pol.dat
Polar solvation energy contribution per residue frame wise.
-apcon contrib_apol.dat
Non-polar solvation energy contribution per residue frame wise.
-diff or -nodiff
Default: yes
By default, selection of two atom groups will be prompted. For example, atom group A and B is selected by user. Then, third AB group will be automatically created by combining A and B. Subsequently, all energy calculation will be performed for these three atom groups A, B and AB.
If this option is switched off by -nodiff, selection of only one atom group will be prompted and all energy calculation will be performed on this selected atom group.
-mme or -nomme
Default: yes
By default, van der Waals and electrostatic energy of the selected group/s will be calculated.
To prevent calculation of the vacuum MM energy, this option can be switched off using -nomme.
-pdie 1
Value of solute dielectric constant in the vacuum electrostatic calculation. It should be similar to that of the polar-solvation energy calculation.
-pbsa or -nopbsa
Default: no
To calculate polar or non-polar solvation enerby, use of -pbsa option is required, and additionally an input paramaeter is required with -i option.
-rad bondi
Three keywords are accepted bondi, mbondi and mbondi2 which corresponds to three type of radius discussed in the publication of g_mmpbsa.
-ndots 100
Number of dots per sphere used in the calculation of solvent accessible surface area and volume. Higher will be the number, more will be the accuracy.
-decomp or -nodecomp
Default: no
To calculate energetic contribution of each residue to total binding energy, use of -decomp option is required.
-silent or -nosilent
Default: Yes
When external APBS is used, -silent option can be used to suppress all the messages from APBS program. This option will not work when g_mmpbsa is compiled with APBS libraries.
This script calculates the average binding energy and its standard deviation/error from the output files, which are obtained from g_mmpbsa.
python MmPbSaStat.py [-h] [-mt] [-mf metafile.dat] [-m energy_MM.xvg]
[-p polar.xvg] [-a apolar.xvg] [-bs] [-nbs 500]
[-of full_energy.dat] [-os summary_energy.dat]
[-om meta_energy.dat]
-h, --help
show this help message and exit
-mt, --multiple
If given, calculates for multiple complexes. Need metafile containing path of energy files
-mf metafile.dat, --metafile metafile.dat
Metafile containing path to energy files of each complex in a row obtained from g_mmpbsa in following order: [MM file] [Polar file] [ Non-polar file]
-m energy_MM.xvg, --molmech energy_MM.xvg
Vacuum Molecular Mechanics energy file obtained from g_mmpbsa.
-p polar.xvg, --polar polar.xvg
Polar solvation energy file obtained from g_mmpbsa.
-a apolar.xvg, --apolar apolar.xvg
Non-Polar solvation energy file obtained from g_mmpbsa.
-bs, --bootstrap
If given, Enable Boot Strap analysis to calculate standard error.
-nbs 500, --nbstep 500
Number of boot strap steps for average energy and standard error calculation.
-of full_energy.dat, --outfr full_energy.dat
Energy File: All energy components in function of time.
-os summary_energy.dat, --outsum summary_energy.dat
Final Energy File: Summary of energy components.
-om meta_energy.dat, --outmeta meta_energy.dat
Final Energy File for Multiple Complexes: Complex wise net binding energy.
This scripts calculate final contribution energy of each residue from individual energetic terms obtained from the g_mmpbsa
python MmPbSaDecomp.py [-h] [-m contrib_MM.dat] [-p contrib_pol.dat]
[-a contrib_apol.dat] [-bs] [-nbs 500] [-ct 999]
[-o final_contrib_energy.dat] [-om energyMapIn.dat]
-h, --help
show this help message and exit
-m contrib_MM.dat, --molmech contrib_MM.dat
Molecular Mechanics energy contribution file obtained from g_mmpbsa.
-p contrib_pol.dat, --polar contrib_pol.dat
Polar solvation energy contribution file obtained from g_mmpbsa.
-a contrib_apol.dat, --apolar contrib_apol.dat
Non-Polar solvation energy contribution file obtained from g_mmpbsa.
-bs, --bootstrap
If given, Enable Boot Strap analysis to calculate standard error.
-nbs 500, --nbstep 500
Number of boot strap steps for average energy and standard error calculation.
-ct 999, --cutoff 999
Absolute Cutoff in kJ/mol: Energy output above and below this value. If its value is 999, all residues energy will be in output.
-o final_contrib_energy.dat, --output final_contrib_energy.dat
Final output file containing binding energy contribution of each residue.
-om energyMapIn.dat, --outmap energyMapIn.dat
It is input file for energy2bfac. It can be used with energy2bfac to map energy on structure for visualization.
This tool maps the binding energy contribution of each residue on the structure. The energy will be written in the B-factor field of the output PDB file/s. These PDB files can be used with any molecular visualizer and residues can be colored according to their energetic contribution. The molecular visualizer should support method to color residues by the B-factor values.
WARNING: tpr/tpx file should not contain PBC broken molecule. One may check by generating a PDB file with following command:editconf -f topol.tpr -o check.pdb. Check check.pdb file through visualization.
Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-i decomp_energy.dat Input Generic data file
-n index.ndx Input, Opt. Index file
-c complex.pdb Output, Opt. Protein data bank file
-s1 subunit_1.pdb Output, Opt. Protein data bank file
-s2 subunit_2.pdb Output, Opt. Protein data bank file
Option Type Value Description
------------------------------------------------------
-[no]h bool yes Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-s topol.tpr
Input tpr/tpx file of molecule
-n index.ndx
Input atomic index file. User will get choice to select atomic groups
-i decomp_energy.dat
File containing energy contribution of each residue obtained from MmPbSaDecomp.py. One can use -i energyMapIn.dat directly for the input.
-c complex.pdb
Output PDB file of molecular complex taken for the calculation, e.g. protein-ligand, protein-DNA or protein-protein.
-s1 subunit_1.pdb
Output PDB file of first sub-unit in accordance with first atomic group chosen through index file.
-s2 subunit_2.pdb
Output PDB file of second sub-unit in accordance with second atomic group chosen through index file.