G_mmpbsa using GROMACS

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Dear ,

Warm greetings

I was working on determining the binding energy on g_mmpbsa between 3HTB and JZ4 ligand (from GROMACS tutorial- Protein ligand intereaction).

I was using the tutorial template from

but I faced challenge in generating the topology-parameter ( tpr ), atom-index ( ndx ), and trajectory ( xtc ) files.

on top of that when I used

g_mmpbsa -f md_0_10.xtc -s md_0_10.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp

I am getting the following

Fatal error:
reading tpx file (md_0_10.tpr) version 119 with version 103 program

Hi Jeremi,

this is a GROMACS-version issue. The g_mmpbsa was never part of the official GROMACS version and as far as I know, the authors did not update the program to work with newer GROMACS versions. There is two options for you to proceed:

  1. Try to use a .pdb as structure input though, because they don’t depend on gromacs versions. However, mmpbsa might rely on information that is not available in the .pdb. In this case
  2. Use the GROMACS version that g_mmpbsa build on and rebuild a .tpr file for that version and analysis. .xtc and .ndx files are version-independent

It’s a bit clumsy and we’re working on defining better molecule topology file formats to avoid these issues, but that is still some time in the future.

hello everyone,
iam trying to use the same module in gromacs 5.1.2 but getting segmentation fault core dumped error . even with g_mmpbsa -h command

g_mmpbsa -h :-) GROMACS - g_mmpbsa, VERSION 5.1.2 (-:

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GROMACS: g_mmpbsa, VERSION 5.1.2
Executable: /usr/local/bin/g_mmpbsa
Data prefix: /usr
Command line:
g_mmpbsa -h

                       :-)  g_mmpbsa (-:                            
                                                                    
           Authors: Rashmi Kumari and Andrew Lynn                   
           Contribution: Rajendra Kumar                             
                                                                    
   Copyright (C) 2013 - 2016 Rashmi Kumari and Andrew Lynn          

g_mmpbsa is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

g_mmpbsa is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with g_mmpbsa. If not, see http://www.gnu.org/licenses/.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
“AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

                       :-)  g_mmpbsa (-:                            

SYNOPSIS

g_mmpbsa [-f [<.xtc/.trr/…>]] [-s [<.tpr/.gro/…>]] [-i [<.mdp>]]
[-n [<.ndx>]] [-mm [<.xvg>]] [-pol [<.xvg>]] [-apol [<.xvg>]]
[-mmcon [<.dat>]] [-pcon [<.dat>]] [-apcon [<.dat>]] [-b ]
[-e ] [-dt ] [-tu ] [-[no]w] [-xvg ]
[-[no]silent] [-rad ] [-rvdw ] [-[no]mme] [-pdie ]
[-[no]incl_14] [-[no]focus] [-[no]pbsa] [-ndots ] [-[no]diff]
[-[no]decomp]

DESCRIPTION

g_mmpbsa calculates relative binding free energy using the MM-PBSA method for
bio-molecular associations such as protein-protein, protein-ligand,
protein-DNA etc. It calculates three components of the binding energy in
separate files, so that user will have choice to calculate MM, PB and SA
energy values according to their objective. It also calculates contribution of
each residue to the net binding energy and provides information about
important contributing residues to the molecular association.

For more detail, see please visit http://rashmikumari.github.io/g_mmpbsa

OPTIONS

Options to specify input files:

-f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-i [<.mdp>] (grompp.mdp) (Opt.)
grompp input file with MD parameters
-n [<.ndx>] (index.ndx) (Opt.)
Index file

Options to specify output files:

-mm [<.xvg>] (energy_MM.xvg) (Opt.)
xvgr/xmgr file
-pol [<.xvg>] (polar.xvg) (Opt.)
xvgr/xmgr file
-apol [<.xvg>] (apolar.xvg) (Opt.)
xvgr/xmgr file
-mmcon [<.dat>] (contrib_MM.dat) (Opt.)
Generic data file
-pcon [<.dat>] (contrib_pol.dat) (Opt.)
Generic data file
-apcon [<.dat>] (contrib_apol.dat) (Opt.)
Generic data file

Other options:

-b (0)
First frame (ps) to read from trajectory
-e (0)
Last frame (ps) to read from trajectory
-dt (0)
Only use frame when t MOD dt = first time (ps)
-tu (ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg
xvg plot formatting: xmgrace, xmgr, none
-[no]silent (no)
Display messages, output and errors from external APBS program.
Only works with external APBS program
-rad (bondi)
van der Waal radius type: bondi, mbondi, mbondi2, force-field
-rvdw (0.1)
Default van der Waal radius (in nm) if radius not found for any
atom-types
-[no]mme (yes)
To calculate vacuum molecular mechanics energy
-pdie (1)
Dielectric constant of solute. Should be same as of polar solvation
-[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]pbsa (no)
To calculate polar and/or non-polar solvation energy
-ndots (24)
Number of dots per sphere in the calculation of SASA, more dots
means more accuracy
-[no]diff (yes)
Calculate the energy difference between two group otherwise only
calculates for one group
-[no]decomp (no)
Decomposition of energy for each residue

Segmentation fault (core dumped)