Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
✍ Scribed by Ono, Satoshi; Nakajima, Nobuyuki; Higo, Junichi; Nakamura, Haruki
- Book ID
- 101221814
- Publisher
- John Wiley and Sons
- Year
- 2000
- Tongue
- English
- Weight
- 384 KB
- Volume
- 21
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
The C96 and AMBER95 force fields were compared with small model peptides Ac-(Ala) n -NMe (Ac = CH 3 CO, NMe = NHCH 3 , n = 2 and 3) in vacuo and in TIP3P water by computing the free-energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β-and constrained α-helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations.