What is the problem with gmx_mmpbsa atom number out of range error?

As I wrote in GMX_MMPBSA_ ana error - #3 by MagnusL, you would almost certainly get more help from gmx_mmpbsa experts from their mailing lists and groups etc. It is not related to GROMACS as such (even if the name of gmx_mmpbsa might suggest so), so most forum members here cannot help you.