I am running an MMPBSA calculation using g_mmpbsa (VERSION 5.1.2) with GROMACS (VERSION 5.1.2), but I am encountering an issue where the polar solvation energy values are nan in polar.xvg. The output looks like this:
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend “Protein PB energy”
@ s1 legend “8SJZ PB energy”
@ s2 legend “Protein=8SJZ PB energy”
80000.000 -10473.799 nan -10406.622
81000.000 -10706.041 nan -10671.689
82000.000 -10664.577 nan -10603.726
Why is the polar solvation energy calculation giving nan values?
Are there specific grid settings, dielectric values, or PB solver parameters I should adjust?
Could this be due to an issue in the topology file or missing parameters in the system?
I would greatly appreciate any insights, suggestions, or solutions to resolve this issue. If anyone has encountered this problem before and found a fix, please share your approach.
Looking forward to your help.
Best regards,
Suma