# Running gmx\_MMPBSA for gromacs files

**URL:** <https://gromacs.bioexcel.eu/t/running-gmx-mmpbsa-for-gromacs-files/2346>\
**Category:** User discussions\
**Created:** [June 11, 2021, 10:51am UTC](https://gromacs.bioexcel.eu/t/running-gmx-mmpbsa-for-gromacs-files/2346 "2021-06-11T10:51:46Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![alireza.mansouri89](https://avatars.discourse-cdn.com/v4/letter/a/3e96dc/32.png) [@alireza.mansouri89](https://gromacs.bioexcel.eu/u/alireza.mansouri89)\
**Post date:** [June 11, 2021, 10:51am UTC](https://gromacs.bioexcel.eu/t/running-gmx-mmpbsa-for-gromacs-files/2346/1 "2021-06-11T10:51:47Z")

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Dear Gromacs users,

I am trying to calculate binding free energy between protein and ligand using gmx\_MMPBSA package. My trajectory and topology file (stripped of water and ions) were created successfully, however when running gmx\_MMPBSA I get the following error:

"PrmtopError: provided receptor/ligand masks don’t select every atom in the complex topology!

Exiting. All files have been retained."

I will post my mmpbsa input script below if that helps:

Input file for running PB and GB in serial

&general

endframe=50, keep\_files=2,

/

&gb

igb=2, saltcon=0.100,

/

&pb

istrng=0.100,

/

Many thanks for any ideas in advance

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**Author:** ![msvaldes145](https://avatars.discourse-cdn.com/v4/letter/m/57b2e6/32.png) [@msvaldes145](https://gromacs.bioexcel.eu/u/msvaldes145)\
**Post date:** [June 16, 2021, 8:57pm UTC](https://gromacs.bioexcel.eu/t/running-gmx-mmpbsa-for-gromacs-files/2346/2 "2021-06-16T20:57:19Z")

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Hi.  
**gmx\_MMPBSA** is not part of the Gromacs tools package. Please consult our group ([https://groups.google.com/g/gmx\_mmpbsa](https://groups.google.com/g/gmx_mmpbsa)) directly or open an issue on Github ([Issues · Valdes-Tresanco-MS/gmx\_MMPBSA · GitHub](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues)) for proper follow-up  
HTH!  
Mario S.