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)
&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.