In order to calculate the binding energy between protein and DNA, i run g_mmpbsa for my protein-DNA complex and i got big energy value number (-17894.45 kcal/mol). But i think the energy values should be small number. Is there any possibilities that protein-DNA complex will experience a higher energy value when we run MMPBSA??? I have 42bp DNA and the protein size is 232 amino acid residues.
Dear Dhanusha,
The binding energy value you got is a huge. It does not make any sense.
Please use the following link for obtaining normal values:
http://rashmikumari.github.io/g_mmpbsa/Usage.html
I have copied some text from the file in the link:
g_mmpbsa
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
Hoping this will be helpful,
Rafik
Did you solve the problem? I also met with the similar situation when applying g_mmpbsa tool to calculate the protein-DNA system recently. The binding free energy was quite large, especially followed with huge electrostatic contribution. That doesn't make any sense.
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