Table 6.
Average H-bond fraction in GB-neck2 and explicit water simulation for DNA (RNA) duplexes and DNA/protein complex.
| System | explicit water | GB-neck2 | ||
|---|---|---|---|---|
| All base pairs | Skip terminal base pairs | All base pairs | Skip terminal base pairs | |
| DNA (CCAACGTTGG)2 | 94±5 | 100±1 | 93±1 | 98±1 |
| DNA (CGCGAATTCGCG)2 | 95±1 | 100±1 | 88±1 | 98±1 |
| RNA (CCAACGUUGG)2 | 96±2 | 98±1 | 97±1 | 98±1 |
| RNA (CGCGAAUUCGCG)2 | 98±1 | 98±1 | 92±1 | 97±1 |
| DNA seq2 (CTAGGTGGATGACTCATT)2 | 94±1 | 99±1 100±1a |
81±1 | 90±1 99±1a |
| DNA-protein complex (PDB ID: 1GCC) DNA sequence: (TAGCCGCCAGC)2 |
94±1 | 99±1 99±1a |
88±1 | 91±1 99±1a |
For DNA and RNA duplexes, uncertainties were calculated from independent runs initiated from A and B-forms. For DNA/protein complex (1GCC), the uncertainties were calculated from independent runs with different starting velocities.
a
For DNA systems having A-T base pairs in the terminal (shown in bold), we also report the H-bond fraction excluding the outer 2 or 3 base pairs (shown in italics, see text for details).