Table 4.
Selected water molecules of the 1J7T crystal structure and their MD corresponding water density areas. “+” denotes water density areas higher than 0.22 water molecules per Å3 observed in the position of the corresponding crystallographic water molecule; “−” denotes lack of high water density in this position. Brackets denote water molecules located in part (b) of the RNA duplex.
| water molecule | AMBER_PRO | AMBER_EU | CHARMM_PRO | CHARMM_EU | CHARMM_PRO_PAR | CHARMM_EU_PAR |
|---|---|---|---|---|---|---|
| W1 | + | + | − | − | − | + |
| W4 | + | + | + | + | − | + |
| (W7) | (−) | (−) | (−) | (−) | (−) | (−) |
| W8 (W54) | −(−) | −(−) | −(−) | −(−) | −(+) | −(−) |
| W9 (W2) | − (−) | −(+) | −(−) | −(+) | +(+) | +(+) |
| W12 | − | − | − | − | − | − |
| W13 | − | − | − | − | − | − |
| W14 | − | − | − | − | + | + |
| W15 | − | + | − | − | + | + |
| W19 | − | − | − | − | + | − |
| W20 | − | − | − | − | + | + |
| W25 | + | + | + | + | − | + |
| W27 | − | + | − | − | − | + |
| W28 | − | + | − | − | − | + |
| W32 | − | − | − | − | + | + |
| W44 | − | close | + | + | − | + |
| (W45) | (+) | (+) | (+) | (+) | (+) | (+) |
| W49 | + | + | + | − | − | − |
| W51 | − | + | + | + | + | + |