# Mmpbsa calculation **URL:** \ **Category:** User discussions\ **Created:** [August 24, 2024, 4:33pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976 "2024-08-24T16:33:47Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Sounak\_Biswas](https://avatars.discourse-cdn.com/v4/letter/s/3ec8ea/32.png) [@Sounak\_Biswas](https://gromacs.bioexcel.eu/u/Sounak_Biswas)\ **Post date:** [August 24, 2024, 4:33pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/1 "2024-08-24T16:33:47Z")
GROMACS version: 2023.3 GROMACS modification: Yes/No I have run md simulation on Gromacs version 2023.3. Using those output files (.xtc .tpr .top) i have tried to do MMPBSA calculation but it always show me error . How can i do mmpbsa calculation using the output files of Gromacs version 2023.3 ? Here’s the code link i have used for mmpbsa calculation > **[Home - gmx\_MMPBSA Documentation](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/)** > > gmx\_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files I gave the following command for calculation mpirun -np 4 gmx\_MMPBSA -O -i mmpbsa.in -cs NPT-MD.tpr -ci index.ndx -cg 1 13 -ct 30ns.xtc -cp topol.top ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [August 24, 2024, 4:43pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/2 "2024-08-24T16:43:20Z")
generate tpr for the desired version ---
**Author:** ![Sounak\_Biswas](https://avatars.discourse-cdn.com/v4/letter/s/3ec8ea/32.png) [@Sounak\_Biswas](https://gromacs.bioexcel.eu/u/Sounak_Biswas)\ **Post date:** [August 24, 2024, 4:52pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/3 "2024-08-24T16:52:18Z")
can you please elaborate. ---
**Author:** ![Seyilaxa](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/seyilaxa/32/3136_2.png) [@Seyilaxa](https://gromacs.bioexcel.eu/u/Seyilaxa)\ **Post date:** [August 25, 2024, 8:42am UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/4 "2024-08-25T08:42:24Z")
Try looking at the GMX\_MMPBSA.log file, it gives more specific error messages at the end ---
**Author:** ![Nik](https://avatars.discourse-cdn.com/v4/letter/n/6de8d8/32.png) [@Nik](https://gromacs.bioexcel.eu/u/Nik)\ **Post date:** [August 25, 2024, 9:24am UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/5 "2024-08-25T09:24:19Z")
You have not specified the output in the command line. See the Examples page where you can find examples for your system. The original code is as follows: gmx\_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com\_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL\_RESULTS\_MMPBSA.dat -eo FINAL\_RESULTS\_MMPBSA.csv What type of error do you have? May be it is because of the gromacs version incompatibility (gmx\_mmpbsa uses it own older version of gromacs in condo environment) or some other reasons. ---
**Author:** ![Sounak\_Biswas](https://avatars.discourse-cdn.com/v4/letter/s/3ec8ea/32.png) [@Sounak\_Biswas](https://gromacs.bioexcel.eu/u/Sounak_Biswas)\ **Post date:** [August 26, 2024, 2:46pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/7 "2024-08-26T14:46:02Z")
Error show that some energy terms are undefined.Please check the input structure and trajectory. Here’s the screenshot what does it actually shows. ![Screenshot from 2024-08-23 15-01-43](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/21376008f73708df3eb1b9df5c8f95e2415624f9.png) ---
**Author:** ![Nik](https://avatars.discourse-cdn.com/v4/letter/n/6de8d8/32.png) [@Nik](https://gromacs.bioexcel.eu/u/Nik)\ **Post date:** [August 26, 2024, 3:38pm UTC](https://gromacs.bioexcel.eu/t/mmpbsa-calculation/9976/8 "2024-08-26T15:38:16Z")
Have you used the same version of Gromacs in gmx\_mmpbsa module and for molecular dynamics simulation? If your md files were created in newer version, that it is necessary to add a gmx\_path variable to the mmpbsa.in file: [The input file - gmx\_MMPBSA Documentation](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#miscellaneous-options)