Add explicit water to MMGBSA calculation

[ale94mleon]

10.1021/acs.jcim.7b00347 shows that take into account the ligand hydration shell improves the MMPBSA calculation. This does not add any dramatic extra computational cost:

• Calculate the closest N waters to the ligand.
• Create a temporal index file that includes these water molecules as part of the receptor.
• Run benchmark and check if there are improvements.

[ale94mleon]

Also check: 0.3389/fchem.2018.00043