I just want to use g_mmpbsa tool for protein to protein binding energy calculation. And I had noticed that the trajectory file (*.xtc) didn't have any water or salt molecules in tutorials. Don't g_mmpbsa tools need water and salt components for calculation? or some solvation model had inserted into g_mmpbsa program to be considered. So, please tell me how do I tackle the trajectory file, to keep or discard the water?
Thanks! Please help me!