# Not getting binding energy for each residue of protein-protein complexes

**URL:** <https://gromacs.bioexcel.eu/t/not-getting-binding-energy-for-each-residue-of-protein-protein-complexes/10674>\
**Category:** User discussions\
**Created:** [December 1, 2024, 8:00pm UTC](https://gromacs.bioexcel.eu/t/not-getting-binding-energy-for-each-residue-of-protein-protein-complexes/10674 "2024-12-01T20:00:43Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Devid](https://avatars.discourse-cdn.com/v4/letter/d/22d042/32.png) [@Devid](https://gromacs.bioexcel.eu/u/Devid)\
**Post date:** [December 1, 2024, 8:00pm UTC](https://gromacs.bioexcel.eu/t/not-getting-binding-energy-for-each-residue-of-protein-protein-complexes/10674/1 "2024-12-01T20:00:43Z")

</div>

Dear users

I have calculated MMPBSA using the following command:  
gmx\_MMPBSA -O -i mmpbsa.in -cs .tpr -ct .xtc -ci index.ndx -cg 19 20 -cp topol.top -o FINAL\_RESULTS\_MMPBSA.dat -eo FINAL\_RESULTS\_MMPBSA.csv

where mmpbsa.in :  
Sample input file for decomposition analysis  
This input file is meant to show only that gmx\_MMPBSA works. Althought,  
we tried to used the input files as recommended in the Amber manual,  
some parameters have been changed to perform more expensive calculations  
in a reasonable amount of time. Feel free to change the parameters  
according to what is better for your system.

&general  
sys\_name=“Decomposition”,  
startframe=0,  
endframe=2000,  
forcefields=“CHARMM36”  
/  
&gb  
igb=5, saltcon=0.150,  
/  
#make sure to include at least one residue from both the receptor  
##and ligand in the print\_res mask of the &decomp section.  
##this requirement is automatically fulfilled when using the within keyword.  
##[Re: [AMBER] Is there any problem with this input file? from Bill Miller III on 2013-08-05 (Amber Archive Aug 2013)](http://archive.ambermd.org/201308/0075.html)  
&decomp  
idecomp=2, dec\_verbose=3,  
print\_res=“within 4”

The issue is that it didn’t provide the energy values for each residue. Could anyone suggest whether I am doing something wrong? Any suggestions for resolving this would be highly appreciated.