gmx_MMPBSA -O -i
mmpbsa.in
-cs gromacs.pdb -ci new_index.ndx -cg 1 2 -ct new.xtc -cp gromacs.top
-o FINAL_RESULTS_MMPBSA1.dat -eo FINAL_RESULTS_MMPBSA1.csv
Sample input file for PB calculation
This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use 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
startframe=500,
endframe=2000,
keep_files=2,
temperature=310,
interval=5,
#strip_mask=":WAT,Na+",
# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only
# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set
PBRadii=3,
/
&pb
# calculation
istrng=0.100,inp=1, fillratio=4.0, radiopt=0,
/
I am getting error InputError: Unknown variable strip_mask in &general