# G\_mmpbsa using GROMACS **URL:** \ **Category:** User discussions\ **Created:** [December 7, 2020, 6:57pm UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-using-gromacs/1216 "2020-12-07T18:57:24Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Jeremi](https://avatars.discourse-cdn.com/v4/letter/j/7feea3/32.png) [@Jeremi](https://gromacs.bioexcel.eu/u/Jeremi)\ **Post date:** [December 7, 2020, 6:57pm UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-using-gromacs/1216/1 "2020-12-07T18:57:24Z")
GROMACS version: GROMACS modification: Yes/No Here post your question 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 > **[g\_mmpbsa](https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html)** 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 ---
**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\ **Post date:** [December 8, 2020, 1:07pm UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-using-gromacs/1216/2 "2020-12-08T13:07:54Z")
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. ---
**Author:** ![Yogesh](https://avatars.discourse-cdn.com/v4/letter/y/49beb7/32.png) [@Yogesh](https://gromacs.bioexcel.eu/u/Yogesh)\ **Post date:** [April 14, 2021, 6:26am UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-using-gromacs/1216/3 "2021-04-14T06:26:29Z")
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 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. 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/](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](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) ---
**Author:** ![garg.8](https://avatars.discourse-cdn.com/v4/letter/g/f6c823/32.png) [@garg.8](https://gromacs.bioexcel.eu/u/garg.8)\ **Post date:** [July 29, 2023, 1:19pm UTC](https://gromacs.bioexcel.eu/t/g-mmpbsa-using-gromacs/1216/4 "2023-07-29T13:19:49Z")
g\_mmpbsa tool can be beneficial for protein ligand simulation using gromos54a7?