g_mmpbsa run

g_mmpbsa run calculates binding energy of bio-molecular 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 calculate either MM, PB and SA energy values or all energy terms according to their objectives. The tool also gives residue wise contribution to total binding energy which will provide information about important contributing residues to the molecular association.

Execute following command to get full help

g_mmpbsa run -h

Warning

On MacOS, external APBS is required to run this command. If APBS is not installed, the command will fail with an error message.

• Use Homebrew to install APBS on MacOS (brew install brewsci/bio/apbs).

• Define APBS environment variable, e.g. export APBS=$(brew --prefix apbs)/bin/apbs.

Command summary

g_mmpbsa run [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
             [-i [<.mdp>]] [-ipdb [<.pdb>]] [-opdb [<.pdb>]] [-mm [<.xvg>]]
             [-pol [<.xvg>]] [-apol [<.xvg>]] [-mmcon [<.dat>]]
             [-pcon [<.dat>]] [-apcon [<.dat>]] [-o [<.xvg>]] [-os [<.csv>]]
             [-ores [<.csv>]] [-b <time>] [-e <time>] [-dt <time>]
             [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-sf <file>]
             [-selrpos <enum>] [-seltype <enum>] [-unit1 <selection>]
             [-unit2 <selection>] [-rvdw <real>] [-pdie <real>]
             [-ndots <int>] [-[no]mme] [-[no]ddc] [-[no]pbsa] [-[no]diff]
             [-[no]decomp] [-[no]incl_14] [-[no]focus] [-[no]silent]

Options summary

Options to specify input files

Option	Default	File type
-f [<.xtc/.trr/…>]	traj.xtc	Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
-s [<.tpr>]	topol.tpr	Input structure: tpr
-n [<.ndx>]	index.ndx	Extra index groups. Should contain index group of first and second sub-units.
-i [<.mdp>]	mmpbsa.mdp	Input parameters for PBSA calculations.
-ipdb [<.pdb>]	input.pdb	Input pdb file to dump residue energy in b-factor field. If not provided, input tpr file will be used.

Options to specify output files

Option	Default	File type
-opdb [<.pdb>]	energy.pdb	Output PDB file with residue energy in b-factor field.
-mm [<.xvg>]	energy_MM.xvg	Vaccum MM energy as a function of time
-pol [<.xvg>]	polar.xvg	Polar solvation energy as a function of time
-apol [<.xvg>]	apolar.xvg	Apolar solvation energy as a function of time
-mmcon [<.dat>]	residues_MM.dat	Vacuum MM energy contribution to binding
-pcon [<.dat>]	residues_polar.dat	Polar solvation energy contribution to binding
-apcon [<.dat>]	residues_apolar.dat	Apolar solvation energy contribution to binding
-o [<.xvg>]	binding_energy.xvg	Final binding energy and its components
-os [<.csv>]	energy_summary.csv	Summary of binding energy over all frames
-ores [<.csv>]	residues_energy_summary.csv	Summary of binding energy contributions of residues over all frames

Other options

Option	Default	Description
-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 if t MOD dt == first time (ps)
-tu <enum>	ps	Unit for time values: fs, ps, ns, us, ms, s
-fgroup <selection>		Atoms stored in the trajectory file (if not set, assume first N atoms)
-xvg <enum>	xmgrace	Plot formatting for xvg file: xmgrace, xmgr, none
-sf <file>		Provide selections from files
-selrpos <enum>	atom	Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-seltype <enum>	atom	Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-unit1 <selection>		Select protein or first group
-unit2 <selection>		Select ligand or second group
-rvdw <real>	0.1	Default van der Waal radius (in nm) if radius not found for any atom-types.
-pdie <real>	1.0	Dielectric constant of solute. Should be same as of polar solvation
-ndots  <int>	24	Number of dots per sphere in the calculation of SASA, more dots means more accuracy
-[no]mme	yes	To calculate vacuum molecular mechanics energy
-[no]ddc	no	To enable distance dependent dielectric constant
-[no]pbsa	no	To calculate polar and/or non-polar solvation energy
-[no]diff	yes	Calculate the energy difference between two group otherwise only calculates for one group
-[no]decomp	no	Number of dots per sphere in the calculation of SASA, more dots means more accuracy
-[no]incl_14	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	no	To enable focusing on the specfic region of molecule, group of atoms must be provided in index file
-[no]silent	no	Display messages, output and errors from external APBS program

Options to specify input files

-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 linksP:

• PBC

• gmx trjconv

-s topol.tpr

Input tpr/tpx file of molecule.

Note

-s only accept tpr/tpx file as input. PDB/GRO file is not allowed as it does not contain force-field parameters required for the MM/PBSA calculations.

-n index.ndx

Input atomic index file. The idex file should contain index groups of first (-unit1) and second (unit2) sub-units.

-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 Parameters

• Non-polar Solvation Parameters

-ipdb input.pdb

Optional input pdb file to dump residue energy in b-factor field. If not provided, input tpr file will be used.

Options to specify output files

-opdb energy.pdb

Output PDB file with residue energy in b-factor field.

-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 components for each group and their complex is calculated. Final binding energy can be calculated later using the g_mmpbsa average sub-command.

-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 their 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 their complex.

-mmcon residues_MM.dat

Vacuum MM van der Waals and electrostatic energy contribution per residue per frame/snapshot.

-pcon residues_polar.dat

Polar solvation energy contribution per residue frame wise.

-apcon residues_apolar.dat

Non-polar solvation energy contribution per residue frame wise.

-o binding_energy.xvg

Final binding energy and its components frame wise.

-os energy_summary.csv

Summary of all energy terms as average and standard deviation. These files can be opened by MS Excel or any other software supporting CSV file.

The output file has following rows and columns:

"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

Summary of binding energy contributions (both average and standard deviation) of residues over all frames. These files can be opened by MS Excel or any other software supporting CSV file.

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,
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